chemistry living and systems: 123.101 lecture 1
DESCRIPTION
123.101 Chemistry & Living Systems: Unit 1 Lecture 1 from Gareth Rowlands Section - Any comments would be greatly appreciated.TRANSCRIPT
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Chemistrya n d l i v i n g s y s t e m s
Gareth Rowlands123.101
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chemistryanintroductionto
and...
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...howitrelatestoliving
things
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the study guide contains all the information you need
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my lectures contain explanationand examples
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but as I’m not here...
...the Prof will have to do!
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my notes are available from:www.massey.ac.nz/~gjrowlan/teaching.html
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my notes are available from:http://www.slideshare.net/gjr2323
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Slideshare is an awesome resource for learning about presentations
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©Noukka Signe@Flickr
read each chapter in advance
I will give different examples. Do not expect me to read it to you...
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Ready?
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pic: Aquarium of the Pacific
Unit One Part 1: introduction
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pic: Aquarium of the Pacific
Unit One Part 1: introductionthese are not random
pictures; the molecule is a potential painkiller
called epibatidine which is isolated from poison
dart frogs...
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why do we need organic chemistry?
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why do we need organic chemistry?
...because its fun??
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why do we need organic chemistry?
...it keeps me in a job?Or...
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i f we want to understand living systems...
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w e n e e d t o understand the individual organs...
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...to understand organs, we have to understand cells...
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...and still we have to get smaller and
smaller...
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N
NN
N
Me
Me
MeHO2C(H2C)2
Me
HO2C(H2C)2
Fe
...and to do this we must understand the molecules that make up these systems
haem
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but we don't need to get carried away...
Image Credit: NIST/University of Colorado
...lets stop with atoms & electrons!And none of this maths malarkey.
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simple chemical principles control
biology
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isomers and the v isua l cascade
Me Me
Me Me
Me
NOpsin
HRhodopsin11-cis-retinal
(aldehyde not imine)
Me Me
Me
Me
NOpsin
H
Me
all trans-retinalstarts VISUAL CASCADE
photon
1112
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$chemistry and medicine
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penicillin Gantibacterial
HN
O N
S
O
H
CO2H
MeMe
http://staff.science.uva.nl/~dcslob/lesbrieven/maarten/Bacterien.html
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penicillin Gantibacterial
HN
O N
S
O
H
CO2H
MeMe
http://staff.science.uva.nl/~dcslob/lesbrieven/maarten/Bacterien.html
Chemistry explains how penicillin blocks
bacterial cell wall synthesis.
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N OHN
O
F
OH OH O
MeMe
Ca2+
2
Liptorcholesterol treatmentUS$ 12.9 billion
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the language of chemistry...
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the language of chemistry...
First we need to be able to communicate
with each other...
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the language of chemistry...
There are three ways of talking about
chemicals...
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SYMBOLICchemical formulae
MICROSCOPICatoms &
molecules
MACROSCOPICbulk
properties
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©DC Comics
macroscopicrepresentation
physical properities
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©DC Comics
macroscopicrepresentation
physical properitiesobviously important
(if you happen to get dunked in a vat
of the stuff)
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©DC Comics
macroscopicrepresentation
physical properities
but ignored in this lecture...lets just
leave it for the lab...
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how do we represent molecules?
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microscopic representation
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microscopic representation
how we represent the actual molecules
themselves...
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molecular orbital representation
hexane
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molecular orbital representation
hexane
electrons spread over entire molecule...true but not very useful!
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hexane
space filling representation
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hexane
space filling representation
shows us the atoms and their relative
size...but bonds hard to see
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hexane
ball and stick representation
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hexane
ball and stick representation
atoms, bonds, shape, it has it all. Time
consuming to draw so...
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symbolic representation
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symbolic representation
quick and dirty ways to represent molecules
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C3H7empirical formula
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C3H7empirical formula
just the ratio of atoms...
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C3H7empirical formulaempirical formula
C3H7C6H14
C9H21
C12H28C15H35C18H42 C21H49
C24H56C27H63 C30H70
C33H77
...too many possibilities!
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molecular formula
C6H14
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molecular formula
C6H14exact number of atoms...
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molecular formula
C6H14molecular formula
HC
CC
CC
CH
H H
H H
H H
H H
H H
H H
HC
CC
CC
H
H H
C H
H H
H H
H H
HHH
HC
CC
CC
H
H H
H H H H
H HCH H
H
HH
CC
CC
HH H
C H
H C
H HH
HH
HH H
...but not how they are connected
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condensedformula
CH3CH2CH2CH2CH2CH3
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condensedformula
CH3CH2CH2CH2CH2CH3bonding sorted...
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condensedformula
CH3CH2CH2CH2CH2CH3
condensedformula
HC
CC
CH
H H
C H
H C
H HH
HH
HH H
(CH3)2CHCH(CH3)CH3N
N
Me
MeO
O
N
NMe
...but bulky...and some structures
would be confusing!
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structural formula
HC
CC
CC
CH
H H
H H
H H
H H
H H
H H
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structural formula
HC
CC
CC
CH
H H
H H
H H
H H
H H
H H
now we’re talking; atoms, bonding,
shape. It has it all. But...
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structural formula
HC
CC
CC
CH
H H
H H
H H
H H
H H
H H
structural formula
N
OMe
N
OH
HCN
CCC
HC
HCCH
CCH
O
CH C
HN CH2
CH2H2C CH
H2CCH
HC
H2COH
CH3
...can be messy and time consuming...
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skeletal (structural) formula
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skeletal (structural) formula
Quick, easy and tells me
everything...but do you understand what it means?
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other representations
CC
C
CC
H
O
HH
H HH
H
HH
H
H
OCHO
CHOH
CH3
OHEt
Ph
H
CH3
OH
H
HO
CH3HPh
Et H
Fischer projection
Newman projection
Sawhorse projection
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do not use this representation!
H C C C C C C HH
H
H
H
H
H
H
HH
HH
H
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do not use this representation!
H C C C C C C HH
H
H
H
H
H
H
HH
HH
H
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©Lucasfilms
...key to this course is understanding / interpreting these
symbols
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understanding skeletal (structural) formulae
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4CARBON
HC
HHH
C CH
H H
H
CCO
H
H H
OH
H C C H
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4CARBON
HC
HHH
C CH
H H
H
CCO
H
H H
OH
H C C H
carbon always has four bonds...
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©ultraBobban@Flickr
why? a good question & one we
will partially answer later
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1HYDROGEN
HC
HHH
C CH
H H
H
CCO
H
H H
OH
CCC
H NO
OH
HH
H
H H
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1HYDROGEN
HC
HHH
C CH
H H
H
CCO
H
H H
OH
hydrogen always has one bond...
CCC
H NO
OH
HH
H
H H
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2OXYGEN
HC
CO
H H
H HH
CCCOC
HH
HH
HH
HH
CCC
H NO
OH
HH
H
H H
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3NITROGEN
CC
NC
H
H HH
HH
C CH
HH N
CCC
H NO
OH
HH
H
H H
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so how do we draw skeletal formulae?
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allC CHcan be removedand
NH
HN
HN
NH
HN
NH
HN
OO
O
O
O
HO OHOH
O O
O
NH2
OHHO
O
Cl
Cl
O
HOHO
OH
OO
NH2OH
O
Vancomycin
O
HO
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allC CHcan be removedand
NH
HN
HN
NH
HN
NH
HN
OO
O
O
O
HO OHOH
O O
O
NH2
OHHO
O
Cl
Cl
O
HOHO
OH
OO
NH2OH
O
Vancomycin
O
HO
assume each corner is a carbon...
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allC CHcan be removedand
NH
HN
HN
NH
HN
NH
HN
OO
O
O
O
HO OHOH
O O
O
NH2
OHHO
O
Cl
Cl
O
HOHO
OH
OO
NH2OH
O
Vancomycin
O
HO...and it will always have four bonds.
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example one
HC
CC
CHH H
H H
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example one
HC
CC
CHH H
H H
CC
CC
– H
remove H
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example one
HC
CC
CHH H
H H
CC
CC
– H – Cnow remove C
![Page 80: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/80.jpg)
example two
CC
CCC
CHH
H
HH
H
![Page 81: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/81.jpg)
example two
CC
CCC
CHH
H
HH
H
CC
CCC
C
– H
remove H
![Page 82: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/82.jpg)
example two
CC
CCC
CHH
H
HH
H
CC
CCC
C
– H – Cnow remove C
![Page 83: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/83.jpg)
example three
CC
O
OH
H
HH
H NH
H
![Page 84: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/84.jpg)
example three
only removeCH
CC
CO
O
N
H
HH
CC
O
OH
H
HH
H NH
H
remove C–HBUT
leave all others!
![Page 85: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/85.jpg)
example three
only removeCH
CC
CO
O
N
H
HH
CC
O
OH
H
HH
H NH
H
This is key. Wecan only remove C–H bonds. We must leave
all others...
![Page 86: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/86.jpg)
example three
– Conly
removeCH
CO2H
NH2
OH
O
NH2CC
CO
O
N
H
HH
CC
O
OH
H
HH
H NH
H
now remove C
![Page 87: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/87.jpg)
examplefourreverse
HOCO2H
NH2
very important
![Page 88: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/88.jpg)
examplefourreverse
HOCO2H
NH2
HOC
CCO2H
NH2C+
add C to corners
![Page 89: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/89.jpg)
examplefourreverse
HOCO2H
NH2
HOC
CCO2H
NH2HO
CC
CO2HH H
H NH2C+ H+ Add H to make all C have four bonds
![Page 90: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/90.jpg)
examplefourreverse
HOCO2H
NH2
HOC
CCO2H
NH2HO
CC
CO2HH H
H NH2C+ H+
HOC
CC
H H
H NH2O
OH
HOC
CC
H H
H NH2O
OH
HOC
CC
H H
H NH2O
OH
remember C has four; O has two
bonds and H has one
![Page 91: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/91.jpg)
2OXYGEN
examplefourreverse
HOC
CC
H H
H NH2O
OH
neither of the O has two bonds
![Page 92: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/92.jpg)
2OXYGEN
examplefourreverse
HOC
CC
H H
H NH2O
OH
O still does not have two bonds. This
structure is wrong
![Page 93: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/93.jpg)
4CARBON
examplefourreverse
HOC
CC
H H
H NH2O
OH
C still does not have four bonds. This
structure is wrong
![Page 94: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/94.jpg)
Functional Groupspages 16-29
©"lapolab"@Flickrlearn them
![Page 95: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/95.jpg)
CO2H
CHO
NC
examplefivereverse
![Page 96: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/96.jpg)
CO2H
CHO
NCC
CC
CO2H
CC
CC
C
CHO
NC
HH
H H H
HH
examplefivereverse
add C to corners and H to make four
bonds
![Page 97: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/97.jpg)
CO2H
CHO
NCC
CC
CO2H
CC
CC
C
CHO
NC
HH
H H H
HH
CC
CC
CC
CC
C
C
C
HH
H H H
HH
O
H
NO
OHexample
fivereverse
now get three bonds to N; two bonds to O and one to H
![Page 98: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/98.jpg)
examplesix
OHCC
CC
CCO2H
O
HO H H OH
H OHC
CC
CC
C
O
HO H H OH
H OHO
HO
OH
OHCC
CC
CCO2H
O
OHOH
OHOHC
CO2H
O
OHOH
OH
C+ H+
![Page 99: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/99.jpg)
what have....we learnt?4organic chemistry is
easy if we can count to...
![Page 100: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/100.jpg)
what have....we learnt?4organic chemistry is
easy if we can count to...
oh, and it’s really important!
![Page 101: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/101.jpg)
before next lecture...
readUnit 1 Part 2 ©Noukka Signe@Flickr
![Page 102: Chemistry Living and Systems: 123.101 Lecture 1](https://reader031.vdocuments.mx/reader031/viewer/2022020110/54720d39b4af9fbe0a8b4ea4/html5/thumbnails/102.jpg)
(Dr. GJ Rowlands)
Acknowledgmentsgareth
wouldlike tothankTrevor Kitson
Massey University& the 101 students
www.massey.ac.nz/~gjrowlan