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Chapter 22
Organic and
Biological Molecules
Chapter 22 Preview
Organic and Biological Molecules
„
Alkanes: Saturated Hydrocarbons
Isomerism, Nomenclature, Reactions of alkanes, Cyclic alkanes
„
Alkenes, Alkynes, and Aromatic Hydrocarbons
Reaction of alkenes and alkynes
„
Hydrocarbon Derivatives
Alcohols, Aldehydes and ketones, Carboxylic acids and esters, and
amines
„
Polymers and Natural Polymers
Properties of polymers, Types of polymers, plymers based on
ethylene, Protein, Carbohydrates, and Nucleic Acids
Introduction
What is Organic Chemistry?
It is defined as the study of hydrocarbons (compounds
of hydrogen and carbon) and their derivatives
Late 18th century:
•Compounds from living organisms - Organic
•Compounds from lifeless matter – Inorganic
•Organic compounds thought to have ‘vital force’
Wöhler 1800-1882
Ammonium cyanate
(from mineral sources)
‘Inorganic’
∆
(Heat)
Urea
(from urine)
‘Organic’
Organic chemicals are universal
Biological matter
•Plants
•Animals
•Microbes
Geological matter
•Fossil Fuels
•Other
Organic
Chemicals
Manufactured
products
Atmospheric
and
cosmic matter
22.1 Alkanes:
Saturated Hydrocarbon
Alkanes
CnH2n+2
consist of only carbon and hydrogen bonded by single covalent bonds single
H
H C H
H
methane
CH3
H H
H C C H
H H
ethane
CH3CH3
H H H H
H C C C C H
H H H H
H H H H H
H C C C C C H
H H H H H
propane
butane
pentane
CH3CH2CH3
CH3CH2CH2CH3
H H H
H C C C H
H H H
C1 – C4 n-alkanes are all gases
Methane main component of natural gas
Propane and butane often stored as compressed gases
Skeletal structure of only carbon atoms
CH3CH2CH2CH2CH3
propane
butane
pentane
n
1
Molecular
Formula
CH4
Structural
formula
H
H C H
Name
methane
Condensed
structural
formula
CH4
H
H H
2
C2H6
H C C H
ethane
CH3CH3
H H
H H H
3
4
5
C3H8
C4H10
H C C C H
propane
H H H
H H H H
H C C C C H
butane
H H H H
C5H12
H H H H H
H C C C C C H
pentane
H H H H H
6
C6H14
CH3CH2CH3
CH3CH2CH2CH3
CH3CH2CH2CH2CH3
H H H H H H
H C C C C C C H
H H H H H H
hexane
CH3CH2CH2CH2CH2CH3
Further members of the series
Heptane
CH3CH2CH2CH2CH2CH2CH3
Octane
CH3CH2CH2CH2CH2CH2CH2CH3
Nonane
CH3CH2CH2CH2CH2CH2CH2CH2CH3
Decane
CH3CH2CH2CH2CH2CH2CH2CH2CH2CH3
Undecane
CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3
Dodecane
CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3
Etc., etc.
Isomerism
Isomers are molecules that have the same molecular
formula but different structures
Extent of structural isomerism in alkanes
Alkane
No. of structural isomers
Methane
Ethane
Propane
1
1
1
Butane
Pentane
Hexane
2
3
5
Decane
75
Pentadecane
4347
Eicosane
366,319
Triacontane
(C30H62)
44 x 109
All known
Pentane C5H12
3 structural isomers
CH3 CH2 CH2 CH2 CH3
CH3
CH3 CH2 CH CH3
CH3
CH3 C CH3
CH3
•All of these based on tetrahedral (sp3 hybridised) Carbon
•No other arrangements of C5H12 possible
Note
CH3
CH3 CH2 CH CH3
CH3
=
CH3 CH CH2 CH3
CH3
=
CH3 CH2 CH
CH3
etc.
How many structural isomers does pentane, C5H12, have?
H
H
H
H
H
H
C
C
C
C
C
H
H
H
H
H
H
H
CH3 H
C
C
H
CH3 H
n-pentane
H
H
H
CH3 H
H
C
C
C
C
H
H
H
H
2-methylbutane
H
C
H
2,2-dimethylpropane
Nomenclature
1. The parent name of the hydrocarbon is that given to the
longest continuous chain of carbon atoms in the molecule.
CH3
CH3
1
CH2
2
CH2
3
CH
4
CH2
5
CH2
2. An alkane minus one hydrogen
atom is called an Alkyl group
CH4
methane
CH3
methyl
6
CH3 4-methylheptane
7
Common Alkyl Groups
Nomenclature
3. When one or more hydrogen atoms are replaced by other
groups, the name of the compound must indicate the
locations of carbon atoms where replacements are made.
Number in the direction that gives the smaller numbers for
the locations of the branches.
CH3
CH3
1
CH
2
CH2
3
CH2
4
CH3
5
CH3
2-methylpentane
CH3
1
CH2
2
CH2
3
CH
4
4-methylpentane
CH3
5
Nomenclature
4. Use prefixes di-, tri-, tetra-, when there is more than one
alkyl branch of the same kind.
CH3
CH3
CH3
CH
CH
CH2
CH2
CH3
1
2
3
4
5
6
2,3-dimethylhexane
CH3
CH3
CH
1
2
CH
3
CH2
CH2
CH3
4
5
6
CH3
3,3-dimethylhexane
Nomenclature
5. Use previous rules for other types of substituents.
CH3
1
Br
NO2
CH
CH
2
3
Names of Common Groups
CH3
4
2-bromo-3-nitrobutane
Br
CH2
1
NO2
CH
CH
2
3
CH3
4
1-bromo-3-nitrobutane
Nomenclature
Rules for Naming Alkanes:
1.
2.
3.
4.
5.
Names after butane are obtained by adding the
suffix –ane to the Greek root for the nyumber of
carbon atoms (pent- for five, hex- for six …)
For a branched carbon hydrocarbons, the name is
given for the longest continuous chain
When they are substituents, the –ane is replaced
with -yl
The positions of substituent groups are specified
by numbering the longest chain starting from the
closest end.
The location and names of each substituent are
followed by the root alkane name and they have to
be listed in alphabetical order, and the prifix di-,
tri- … for multiple.
CH3
CH3
CH3 CH2 C CH2 CH2 C CH2 CH3
CH2 CH2 CH3
H
CH3
CH3
CH3
C CH2 C CH3
H
CH3
2,2,4-Trimethylpentane
CH3
2
C CH3
1
CH2 CH3 H
CH3 3
5
6
4
CH3 CH2 C CH2
2,4-dimethyl-4-ethylhexane
Questions
What is the IUPAC name of the following compound?
CH3
CH3
1
CH
2
C2H5
CH2
3
CH
4
CH2
5
CH2
6
CH2
7
What is the structure of 2-propyl-4-methylhexane?
CH3
8
Alkane Reactions
Combustion reaction
Alkanes are fairly uncreative, but at sufficient high temperature
react vigorously and exothermically with oxygen
CH4 (g) + 2O2 (g)
CO2 (g) + 2H2O (l) ∆H0 = -890.4 kJ
Substitution reaction
CH4 (g) + Cl2 (g)
light
Cl2 + energy
H
Cl• + H
H
H
C
H
Substitution reaction
Cl• + Cl•
H
H
H
C• + Cl
CH3Cl (g) + HCl (g)
Cl
•C
Formation of unsaturated
hydrocarbons
H + HCl
H
H
H
C
H
CH3CH3 ÆCH2=CH2+H2
Using Cr2O3 at high temperature
Cl + Cl•
Freons CFxCl4-x
Cyclic Alkanes
Alkanes whose carbon atoms are joined in rings are called Cyclic
Alkanes. They have the general formula CnH2n where n = 3,4,…
22.2 Alkene and Alkyne
Alkene have the general formula CnH2n where n = 2,3,…
• contain at least one carbon-carbon double bond and the
systematic names are ethene, propene, …..
CH
CH2
CH2
CH3
CH3
CH
CH
CH3
1-butene
2-butene
• have restricted rotation around the double bond to produce
cis-trans isomerisms
Cl
Cl
C
C
H
H
cis-dichloroethylene
Cl
H
C
C
H
Cl
trans-dichloroethylene
Alkyne
Alkyne have the general formula CnH2n-2 where n = 2,3,4,…
• contain at least one carbon-carbon triple bond and the
systematic names are ethyne, propyne, …..
C CH2 CH3
C CH3
CH3 C
1-butyne
2-butyne
Reactions of alkenes and alkynes
Hydrogenation
CH CH (g) + H2 (g)
CH2 CH2 (g)
Halogenation Reactions
CH
CH2 CH2 (g) + Br2 (g)
CH2Br CH2Br (g)
Polymerization
Small molecules are joined together to form large molecules
22.3 Aromatic Hydrocarbons
A special class of cyclic unsaturated hydrocarbons
H
•Benzene is the simplest
H
C
C
•The delocalized p-electrons
make it different than
C
H
the other unsaturated
hydrocarbons
•Benzene does not present
the addition reactions
H
C
C
C
H
H
H
H
H
C
C
C
C
C
C
H
H
H
Aromatic Compound Nomenclature
ethylbenzene
CH2CH3
aminobenzene
NH2
Cl
chlorobenzene
6
2
5
3
4
nitrobenzene
Br
Br
1
NO2
Br
Br
1,2-dibromobenzene
1,3-dibromobenzene
Aromatic Compound Reactions
Substitution reaction
H
Br
H
H
+ Br2
H
FeBr3
H
H
H
H
H
H
H
H
+ CH3CH2Cl
H
+ HBr
catalyst
H
H
H
H
CH2CH3
H
H
AlCl3
+ HCl
catalyst
H
H
H
Polycyclic Aromatic Hydrocarbons
22.4 Hydrocarbon Derivatives
Hydrocarbons that have
additional atoms or
groups different than
Carbon and hydrogen
(functional group)
The common functional
groups are….
They exhibit
characteristic chemistry
Alcohols contain the hydroxyl functional group
and have the general formula R-OH.
The systematic name is obtained
from parent alkane by removing
the final letter –e and adding –ol.
Biological production of ethanol
C6H12O6 (aq)
enzyme
2CH3CH2OH (aq) + 2CO2 (g)
Commercial production of ethanol
CH2 CH2 (g) + H2O (g)
H2SO4
CH3CH2OH (g)
Metabolic oxidation of ethanol
CH3CH2OH
alcohol dehydrogenase
CH3CHO + H2
Aldehyde and Ketones
They contain carbonyl functional group.
O
• Aldehyde have the general formula R C H
O
• Ketone have the general formula R C R’
The systematic name of aldehyde is obtained from parent alkane by
removing the final letter –e and adding –al, and for ketone also by
removing the final letter –e and adding –one.
O
O
O
H C H
H C CH3
H3C C CH3
___________
___________
___________
Carboxylic acids and Esters
they contain the carboxyl functional group.
The systematic name
is obtained from parent
alkane by removing
the final letter –e and
adding –oic.
The esters are formed, if carboxylic acid reacts with alcohol:
O
CH3COOH + HOCH2CH3
CH3 C O CH2CH3 + H2O
ethyl acetate
The systematic name is obtained from parent alkane by removing the
final letter –oic and adding –oate of the acid, e.g., ethyl ethanoate.
Amines
They are organic bases with the general formula RNH2
The common names are often
used for simple amines, and the
systematic name is obtained by
using the name amino for each –
NH2 group, e.g., 2-aminobutane
They are used for making dyes and
their main reaction is acid-base:
CH3NH2 + H2O
CH3CH2NH2 + HCl
RNH3+ + OHCH3CH2NH3+Cl-
22.5 Polymers
A polymer is a high molar mass molecular compound made
up of many repeating chemical units.
Naturally occurring polymers
•Proteins
•Nucleic acids
•Cellulose
•Rubber
Synthetic polymers
•Nylon
•Dacron
•Lucite
The simple repeating unit of a polymer is the monomer.
Homopolymer is a polymer made up of only one type of
monomer
( CH2 CH )n
( CH2 CH2 )n
( CF2 CF2 )n
Cl
Teflon
Polyethylene
PVC
Stereoisomers of Polymers
R groups on same
side of chain
Isotactic
R groups alternate
from side to side
Syndiotactic
R groups disposed
at random
Atactic
22.2
Proteins
Amino acids are the basic structural units of proteins. An
amino acid is a compound that contains at least one amino
group (-NH2) and at least one carboxyl group (-COOH)
H O
H O
+H
3N
C C O- + +H3N C C OR2
R1
Peptide bond
H O
H O
+H
3N
C C N C C O- + H2O
R1
H R2
22.3
22.3
Protein Structure
Carbon
Nitrogen
Oxygen
R group
The structure is
held in position by
intramolecular
hydrogen bonds
(………)
Hydrogen
22.3
Protein Structure
22.3
Protein Structure
Intermolecular Forces in a Protein Molecule
ionic forces
hydrogen
bonds
dispersion
forces
ionic forces
dispersion
forces
dispersion
forces
dipole-dipole
forces
22.3
Hydrogen Bonds in Parallel and Antiparallel β-pleated Sheets
22.3
Protein Structure
The structural changes that occur when oxygen binds to the
heme group in hemoglobin.
22.3
Nucleic Acids
Nucleic acids are high molar mass polymers that play an
essential role in protein synthesis.
1. Deoxyribonucleic acid (DNA)
2. Ribonucleic acid (RNA)
DNA molecule has 2 helical strands.
Each strand is made up of nucleotides.
22.4
The Components of the Nucleic Acids DNA and RNA
22.4
Base-Pair Formation by Adenine and Thymine and by
Cytosine and Guanine
22.4
Chemistry In Action: DNA Fingerprinting
22.4