Organic and Biological Molecules

1
Organic and Biological Molecules

• Chapter 22

2
Organic Chemistry and Biochemistry

• The study of carbon-containing
• compounds and their properties.
• The vast majority of organic
• compounds contain chains of rings
• of carbon atoms.
• The study of the chemistry of living
• matter

3
Hydrocarbons

• compounds composed of carbon and hydrogen.
• Saturated compounds (alkanes) have the maximum
  number of hydrogen atoms attached to each carbon
  atom
• Saturated carbon-carbon bonds are all single -
  alkanes CnH2n2

4

• Unsaturated compounds have fewer hydrogen atoms
  attached to the carbon chain than alkanes
• Unsaturated They contain carbon-carbon multiple
  bonds (double or triple)

5
22.1 Alkanes Saturated hydrocarbons

• Saturated hydrocarbons, CnH2n2
• Saturated because they cant take any more
  hydrogen atoms
• Straight chains are H3C(CH2)n2CH3
• Waxes, oils, fuel gases as n decreases.

6
Alkanes Saturated Hydrocarbons

• Hydrocarbons are molecules composed of carbon
  hydrogen
• Each carbon atom forms 4 chemical bonds
• A saturated hydrocarbon is one where all C - C
  bonds are single bonds the molecule contains
  the maximum number of H-atoms
• Saturated hydrocarbons are called ALKANES

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Methane is a tetrahedral molecule
8
The Lewis structure of ethane.
9
A ball-and-stick model of ethane.
10
Propane
11
Butane
12
The First 10 Normal Alkanes

• Name Formula M.P. B.P. Structural Isomers
• Methane CH4 -183 -162 1
• Ethane C2H6 -172 -89 1
• Propane C3H8 -187 -42 1
• Butane C4H10 -138 0 2
• Pentane C5H12 -130 36 3
• Hexane C6H14 -95 68 5
• Heptane C7H16 -91 98 9
• Octane C8H18 -57 126 18
• Nonane C9H20 -54 151 35
• Decane C10H22 -30 174 75

C1 - C4 are Gases at Room Temperature
C5 - C16 are Liquids at Room Temperature
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The C-H Bonds in Methane
14
IUPAC Rules for Naming Branched Alkanes

• Find and name the parent chain in the hydrocarbon
  - this forms the root of the hydrocarbon name
• Number the carbon atoms in the parent chain
  starting at the end closest to the branching
• Name alkane branches by dropping the ane from
  the names and adding yl. A one-carbon branch
  is called methyl, a two-carbon branch is
  ethyl, etc
• When there are more than one type of branch
  (ethyl and methyl, for example), they are named
  alphabetically
• Finally, use prefixes to indicate multiple
  branches

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Rules for Naming Alkanes

• 1. For alkanes beyond butane, add -ane to the
  Greek root for the number of carbons.
• C-C-C-C-C-C hexane
• 2. Alkyl substituents drop the -ane and add
  -yl
• -C2H5 is ethyl

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Rules for Naming Alkanes

• 3. Positions of substituent groups are specified
  by numbering the longest chain sequentially.
• C
• ??
• C-C-C-C-C-C
• 3-methylhexane
• Start numbering at the end closest to the
  branching
• 4. Location and name are followed by root alkane
  name. Substituents in alphabetical order and use
  di-, tri-, etc.

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Normal vs Branched Alkanes

• Normal alkanes consist of continuous chains of
  carbon atoms
• Alkanes that are NOT continuous chains of carbon
  atoms contain branches
• The longest continuous chain of carbons is called
  the parent chain

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Structural Isomerism

• Structural isomers are molecules with the same
  chemical formulas but different molecular
  structures - different connectivity.
• They arise because of the many ways to create
  branched hydrocarbons.

n-pentane, C5H12
2-methlbutane, C5H12
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Isomer Naming

• Older conventions would have that as isooctane,
  but a good IUPAC name results from the following
• Name the longest C chain (pentane)
• List the side groups in alphabetical order with
  Greek prefixes (trimethylpentane)
• Supply (smallest possible) positional indices
  (2,2,4 trimethylpentane)

21
Example Show the structural formula
of 2,2-dimethylpentane

• The parent chain is indicated by the ROOT of the
  name - pentane. This means there are 5 carbons
  in the parent chain.

• dimethyl tells us that there are TWO methyl
  branches on the parent chain. A methyl branch is
  made of a single carbon atom.
• 2,2- tell us that BOTH methyl branches are on
  the second carbon atom in the parent chain.

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Example Structural formula of
3-ethyl-2,4-dimethylheptane?

• The parent chain is indicated by the ROOT of the
  name - heptane. This means there are 7 carbons
  in the parent chain.

• 2,4-dimethyl tells us there are TWO methyl
  branches on the parent chain, at carbons 2 and
  4.
• 3-ethyl- tell us there is an ethyl branch
  (2-carbon branch) on carbon 3 of the parent
  chain.

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Example 2,3,3-trimethyl-4-propyloctane

• The parent chain is indicated by the ROOT of the
  name - octane. This means there are 8 carbons
  in the parent chain.

• 2,3,3-trimethyl tells us there are THREE methyl
  branches - one on carbon 2 and two on carbon 3.
• 4-propyl- tell us there is a propyl branch
  (3-carbon branch) on carbon 4 of the parent
  chain.

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Example Name the molecules shown

• parent chain has 5 carbons - pentane
• two methyl branches - start counting from the
  right - 2 and 3
• 2,3-dimethylpentane

• parent chain has 8 carbons - octane
• two methyl branches - start counting from the
  left - 3 and 4
• one ethyl branch - 5
• name branches alphabetically

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Reactions of alkanes

• Combustion reactions
• 2C4H10 13 O2 8CO2 10 H2O(g)
• Substitution Reactions

CH4 Cl2 CH3Cl HCl
CH3Cl Cl2 CH2Cl2 HCl
CH2Cl2 Cl2 CH Cl3 HCl
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Dehydrogenation Reactions

• CH3CH3 CH2 CH2

Ethylene
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Cyclic alkanes

• A cycloalkane is made of a hydrocarbon chain that
  has been joined to make a ring.

• Note that two hydrogen atoms were lost in forming
  the ring
• What is the general formula for a cycloalkane?

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Cyclic alkanes, CnH2n

• If the two end Cs lose 1 H each, they have free
  valence to close a ring
• Again, properties similar to straight chains.
• Can now have conformational isomers!
• E.g., BOAT cyclohexane versus CHAIR

29
Cyclohexane - Boat Chair Conformations

• Cyclohexane is NOT a planar molecule. To achieve
  its 109.5 bond angles and reduce angle strain,
  it adopts several different conformations.
• The BOAT and CHAIR (99) are two conformations

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22.2 Alkenes and Alkynes

• Alkenes hydrocarbons that contain a
  carbon-carbon double bond. CnH2n
• CC Ethene
• C?CC propene
• Alkynes hydrocarbons containing a carbon-carbon
  triple bond. CnH2n-2
• C ?C Ethyne
• C?C?C?C?C 2-pentyne

31
Alkenes Alkynes

• The suffix for the parent alkane chains are
  changed from ane to ene and yne
• e.g. ethene, ethyne
• Where it is ambiguous, the BONDS are numbered
  like branches so that the location of the
  multiple bond may be indicated

• Alkenes are hydrocarbons that contain at least
  one carbon-carbon double bond
• Alkynes are hydrocarbons that contain at least
  one carbon-carbon triple bond

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Alkenes, CnH2n

• Cycle formation isnt the only possible result of
  dehydrogenation.
• Adjacent Cs can double bond, CC, making an
  (unsaturated) alkene.

Sp2
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The Bonding in Ethylene
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Nomenclature for Alkenes

• 1. Root hydrocarbon name ends in -ene
• C2H4 CH2CH2 is ethene
• 2. With more than 3 carbons, double bond is
  indicated by the lowest numbered carbon atom in
  the bond.
• CC?C?C is 1-butene

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Alkene Isomers

• While an sp3 CX2Y2 has only 1 isomer,
• (every X and Y is adjacent to all the others)
• the sp2 alkene C2X2Y2 has cis trans isomers
  (where X is or isnt on the same side of as X).
• For longer hydrocarbons, cis trans refer to the
  side the chain extends

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Cis and Trans Isomers

• Double bond is fixed
• Cis/trans Isomers are possible
• CH3 CH3 CH3
• CH CH CH CH
• cis trans CH3

37
Addition Reactions

• in which (weaker) ? bonds are broken and new
  (stronger) ? bonds are formed to atoms being
  added.

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Hydrogenation

• Adds a hydrogen atom to each carbon atom of a
  double bond
• H H H H
• Ni
• HCCH H2 HCCH
• H H
• ethene ethane

CH3-CH3
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Halogenation

• Adds a halogen atom to each carbon atom of a
  double bond
• H H H H
• Ni
• HCCH Cl2 HCCH
• Cl Cl
• ethene dichloro ethane

40
Halogenation Reactions
CH2 CHCH2CH2CH2 Br2

CH2Br CHBrCH2CH2CH2

1,2-dibromopentane
41
Alkynes, CnH2n2

• sp triple bonding makes a rigid 180 segment in a
  hydrocarbon.

• Carbon-carbon triple bonds
• Names end in -yne
• HC?CH ethyne(acetylene)
• HC?C-CH3 propyne

42
The Bonding in Acetylene
43
Naming Alkenes and Alkynes

• When the carbon chain has 4 or more C atoms,
  number the chain to give the lowest number to
  the double or triple bond.
• 1 2 3 4
• CH2CHCH2CH3 1-butene
• CH3CHCHCH3 2-butene
• CH3CH?CHCH3 2-butyne

44
Question

• Write the IUPAC name for each of the following
  unsaturated compounds
• A. CH3CH2C?CCH3
• CH3
• B. CH3CCHCH3 C.

2-pentyne
2-methyl-2-butene
3-methylcyclopentene
45
Question

• Name the following compound

5-ethyl-3-heptyne
46
Additions reactionsHydrogenation and Halogenation

• Hydrogens and halogens also add to the triple
  bond of an alkyne.

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22.3 Aromatic hydrocarbonsUnsaturated Cyclic
hydrocarbons

• Alternating single/double bond
• cycles occur in many organic molecules
• This class is called aromatic (by virtue of
  their aroma).
• The ? structure is often preserved in their
  chemical reactions they dont add, they
  substitute instead.

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Lewis structures for the benzene ring.
49
Benzene C6H6
sp2
sp2
sp2
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Shorthand notation for benzene rings
51
The bonding in the benzene ring is a combination
of different Lewis structures.
52
Aromatic Hydrocarbons

• Substitution reaction

Nitroobenzene
Chlorobenzene
-NO2
-CH3
Cl2
HNO3
Toluene
HNO3
CH3Cl
benzene
HCl H2O HCl
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Nomenclature of benzene derivatives
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More Complex Aromatic Systems
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22.4 Hydrocarbon Derivatives(Functional Groups)

• Molecules that are fundamentally hydrocarbons but
  have additional atoms or group of atoms called
  functional groups
• Part of an organic molecule where chemical
  reactions take place
• Replace an H in the corresponding alkane
• Provide a way to classify organic compounds

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The Common Functional Groups

• Class General Formula
• Halohydrocarbons R?X
• Alcohols R?OH
• Ethers R?O?R?
• Aldehydes

58

• Class General Formula
• Ketones
• Carboxylic Acids
• Esters
• Amines

59
Some Types of Functional Groups

• Haloalkane -F, -Cl, -Br CH3Cl
• Alcohol -OH CH3OH
• Ether -O- CH3-O-CH3
• Aldehyde
• Ketone

60
More Functional Groups

• Carboxylic acid -COOH CH3COOH
• Ester -COO- CH3COOCH3
• Amine -NH2 CH3NH2
• Amide -CONH2 CH3CONH2

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Haloahydrocarbons

• An alkane in which one or more H atoms is
  replaced with a halogen (F, Cl, Br, or I)
• CH3Br bromomethane
• Br (methyl bromide)
• CH3CH2CHCH3 2-bromobutane
• Cl
• chlorocyclobutane

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Nomenclature

• Name the following
• bromocyclopentane
• 1,3-dichlorocyclohexane

1
2
3
64
Substituents

• List other attached atoms or groups in
  alphabetical order
• Br bromo, Cl chloro
• Cl Br
• CH3CHCH2CHCH2CH2CH3
• 4-bromo-2-chloroheptane

5
3
2
4
1
65
Nomenclature

• The name of this compound is
• Cl CH3
• CH3CH2CHCH2CHCH3
• 1) 2,4-dimethylhexane
• 2) 4-chloro-5-methylhexane
• 3) 4-chloro-2-methylhexane

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Solution

• The name of this compound is
• Cl CH3
• CH3CH2CHCH2CHCH3
• 3. 4-chloro-2-methylhexane

6
5
3
1
2
4
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Alcohols ROH

• The OH makes alcohol polar enough to hydrogen
  bond.
• Thus, they are water soluble
• Ethanol is a fermentation product acid.

C6H12O6 Glucose
2CH3CH2OH Ethanol
2 CO2

• Methanol is produced industrially by
  hydrogenation
• of carbon monoxide

CO 2H2O CH3OH
Methanol
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Uses of alcohols

• Methanol is used to synthesize adhesives, fibers,
  plastics and recently as motor fuel
• It is toxic to human and can lead to blindness
  and death
• Ethanol can be added to gasoline to form gasohol
  and used in industry as solvent
• Commercial production of ethanol
• CH2CH2 H2O CH3CH2OH

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Classes of alcohols
Alcohols can be classified according to the
number of hydrocarbon fragments bonded to the
carbon where the OH group is attached
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Naming Alcohols

• In IUPAC name, the -e in alkane name is replaced
  with -ol.
• CH4 methane
• CH3OH methanol (methyl alcohol)
• CH3CH3 ethane
• CH3CH2OH ethanol (ethyl alcohol)

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Phenol (Aromatic alcohol)
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More Names of Alcohols

• IUPAC names for longer chains number the chain
  from the end nearest the -OH group.
• CH3CH2CH2OH 1-propanol
• OH
• CH3CHCH3 2-propanol
• CH3 OH
• CH3CHCH2CH2CHCH3 5-methyl-2-hexanol

5
2
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Some Typical Alcohols

• OH
• Rubbing alcohol CH3CHCH3
• 2-propanol (isopropyl alcohol)
• Antifreeze HO-CH2-CH2-OH
• 1,2-ethanediol (ethylene glycol)
• OH
• glycerol HO-CH2-CH-CH2OH

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Example

• Name the following alcohols
• A. OH
• CH3CHCHCH2CH3
• CH3
• OH
• B.

3-methyl-2-pentanol
Cyclobutanol
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Reactions of Alcohols

• Combustion
• CH3OH 2O2 CO2 2H2O Heat
• Dehydration
• H OH
• heat
• H-C-C-H H-CC-H H2O
• H H H H
• alcohol alkene

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Ethers

• Contain an -O- between two carbon groups
• Simple ethers named from -yl names of the
  attached groups and adding ether.
• CH3-O-CH3 dimethyl ether
• CH3-O-CH2CH3 ethyl methyl ether

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Aldehydes and Ketones

• In an aldehyde, an H atom is attached to a
  carbonyl group
• O carbonyl group
• ?
• CH3-C-H
• In a ketone, two carbon groups are attached to a
  carbonyl group
• O carbonyl group
• ?
• CH3-C-CH3

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Naming Aldehydes

• IUPAC Replace the -e in the alkane name -al
• Common Add aldehyde to the prefixes form (1C),
  acet (2C), propion(3), and butry(4C)
• O O O
• ? ? ?
• H-C-H CH3-C-H CH3CH2C-H
• methanal ethanal propanal
• (formaldehyde) (acetaldehyde)
  (propionaldehyde)

methane
ethane
propane
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Aldehydes as Flavorings
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Naming Ketones

• In the IUPAC name, the -e in the alkane name is
  replaced with -one
• In the common name, add the word ketone
• after naming the alkyl groups attached to the
  
• carbonyl group
• O O
• ? ?
• CH3 -C-CH3 CH3-C-CH2-CH3
• Propanone 2-Butanone
• (Dimethyl ketone) (Ethyl methyl ketone)

cyclohexane
propane
butane
Acetone
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Preparation of aldehydes and Ketones

• They are produced by oxidation of alcohols
• CH3CH2OH

Oxidation
acetaldehyde
ethanal
Primary alcohol
Oxidation
acetone
propanone
Secondary alcohol
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Question

• Classify each as an aldehyde (1), ketone (2) or
  neither(3).
• O
• ?
• A. CH3CH2CCH3 B. CH3-O-CH3
• CH3 O
• ?
• C. CH3-C-CH2CH D.
• CH3

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Solution

• Classify each as an aldehyde (1), ketone (2) or
  neither(3).
• O
• ?
• A. CH3CH2CCH3 2 B. CH3-O-CH3 3
• CH3 O
• ?
• C. CH3-C-CH2CH 1 D. 2
• CH3

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Question

• Name the following
• O
• ?
• A. CH3CH2CCH3 B.
• CH3 O
• ?
• C. CH3-C-CH2CH
• CH3

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Solution

• O
• ?
• A. CH3CH2CCH3 B.
• 2-butanone (ethyl methyl ketone)
• CH3 O
• ?
• C. CH3-C-CH2CH
• cyclohexanone
• CH3
• 2,2-dimethylbutanal

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Question

• Draw the structural formulas for each
• A. 3-Methylpentanal
• B. 2,3-Dichloropropanal
• C. 3-Methyl-2-butanone

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Solution

• Draw the structural formulas for each
• CH3 O
  ?
• A. 3-Methylpentanal CH3CH2CHCH2CH
• Br O
• ?
• B. 2,3-Dibromopropanal Br-CH2CHCH
• 
  O
• ?
• C. 3-Methyl-2-butanone CH3CHCCH3
• CH3

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Carboxylic Acids and Esters Carboxyl Group

• Carboxylic acids contain the carboxyl group as
  carbon 1.
• O
• R ??
• CH3 COH CH3COOH
• carboxyl group

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Naming Carboxylic Acids

• Formula IUPAC Common
• alkan -oic acid prefix ic acid
• HCOOH methanoic acid formic acid
• CH3COOH ethanoic acid acetic acid
• CH3CH2COOH propanoic acid propionic acid
• CH3CH2CH2COOH butanoic acid butyric acid

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Naming Rule for Carboxylic acids

• Identify longest chain
• (IUPAC) Number carboxyl carbon as 1
• CH3
• CH3 CHCH2 COOH
• IUPAC 3-methylbutanoic acid

1
4
2
3
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Question

• Give IUPAC name
• A. CH3COOH
• CH3
• B. CH3CHCOOH

2
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Solution

• A. CH3COOH
• ethanoic acid acetic acid
• CH3
• B. CH3CHCOOH
• 2-methylpropanoic acid

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Preparation of carboxylic acids

• Oxidation of primary alcohols
• CH3CH2OH CH3COOH

KMnO4
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Reaction of carboxylic acid with alcohol
Esterification
Alcohol
Carboxylic acid
Ester
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Esters

• In a ester, the H in the carboxyl group is
  replaced with an alkyl group
• O
• ??
• CH3 CO CH3 CH3COO CH3
• ester group

• Esters give fruity odors

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Naming Esters

• The parent alcohol is named first with a yl
  ending
• Change the oic ending of the parent acid to
  ate
• acid alcohol
• O
• ?? methyl
• CH3 CO CH3
• Ethanoate methyl ethanoate (IUPAC)
• (acetate) methyl acetate (common)

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Some esters and their names

• Flavor/Odor
• Raspberries
• HCOOCH2CH3 ethylmethanoate (IUPAC)
• ethylformate (common)
• Pineapples
• CH3CH2CH2 COOCH2CH3
• ethylbutanoate (IUPAC)
• ethylbutyrate (common)

98
Question

• Give the IUPAC and common names of the following
  compound, which is responsible for the flavor and
  odor of pears.
• O
• ??
• CH3 C O CH2CH2CH3

99
Solution

• O
• ?? propyl
• CH3 CO CH2CH2CH3
• propylethanoate (IUPAC)
• propyl acetate (common)

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Question

• Draw the structure of the following compounds
• 3-bromobutanoic acid
• Ethyl propionoate

101
Solution

• A. 3-bromobutanoic acid
• Br
• CH3CHCH2COOH
• B. Ethyl propionoate
• O
• ??
• CH3 CH2 COCH2CH3 CH3CH2COOCH2CH3

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Hydrolysis of esters

• Esters react with water and acid catalyst
• Split into carboxylic acid and alcohol
• O
• ?? H
• H COCH2CH3 H2O
• O
• ??
• H COH HOCH2CH3

-OH
H
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Amines

• Organic compounds of nitrogen N derivatives of
  ammonia
• Classified as primary, secondary, tertiary
• CH3 CH3
• ? ?
• CH3NH2 CH3NH CH3N CH3
• Primary Secondary Tertiary
  
• one N-C two N-C three N-C
• bond bonds bonds

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Naming Amines

• IUPAC aminoalkane Common alkylamine
• CH3CH2NH2 CH3NH CH3
• aminoethane N-methylaminomethane
• (ethylamine) (dimethylamine)
• NH2
• CH3CHCH3
• 2-aminopropane Aniline N-methylaniline
  
• (isopropylamine)

105
Question

• Give the common name and classify
• A. CH3NHCH2CH3
• CH3
• B. CH3CH2NCH3

106
Solution

• A. CH3NHCH2CH3
• ethylmethylamine, (Secondary)
• CH3
• CH3CH2NCH3
• ethyldimethylamine, (Tertiary)

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Question

• Write a structural formula for
• 2-aminopentane
• B. 1,3-diaminocyclohexane

108
Solution

• A. 1-aminopentane
• CH3CH2CH2CH2CH2-NH2
• B. 1,3-diaminocyclohexane

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PolymersPoly many mersparts

• Polymers are large, usually chainlike molecules
  that are built from small molecules called
  monomers joined by covalent bonds
• Monomer Polymer
• Ethylene Polyethylene
• Vinyl chloride Polyvinyl chloride
• Tetrafluoroethylene Teflon

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Some common synthetic polymers, their monomers
and applications
112
Types of Polymerization

• Addition Polymerization monomers add together
  to form the polymer, with no other products.
  (Teflon)
• Condensation Polymerization A small molecule,
  such as water, is formed for each extension of
  the polymer chain. (Nylon)

113
Addition Polymerization
A species with an unpaired electron such as
hydroxyl free radical
The polymerization process Is initiated by a free
radical
Free radical attacks and break The ? bond of
ethylene molecule To form a new free radical

• Repetition of the process thousands of times
  creates a long chain
• polymer
• The process is terminated when two radicals
  react to form a bond
• thus there will be no free radical is
  available for further repetitions.

114
another
(Polythene)

• Depending upon conditions of polymerization,
  the
• product may be branched or linear polyethylene

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Condensation PolymerizationFormation of Nylon
Diamine
Dicarboxylic acid
Dimer

• Small molecule such as H2O is formed
• from each extension of the polymer chain
• both ends are free to react

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Nylon
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Proteins

• Natural polymers made up of ?-amino
• acids (molecular weight from ? 6000 to
• gt1,000,000 g/mol).
• 1. Fibrous Proteins provide structural
  integrity and strength to muscle, hair and
  cartilage.

125
Proteins

• 2. Globular Proteins
• Roughly spherical shape
• Transport and store oxygen and nutrients
• Act as catalysts
• Fight invasion by foreign objects
• Participate in the bodys regulatory system
• Transport electrons in metabolism

126
?-Amino Acids

• ?NH2 always attached to the ?-carbon (the carbon
  attached to ?COOH)
• C ?-carbon

127
Bonding in ?-Amino Acids

• The protein polymer is built by condensation
  reaction
• between amino acids

• 
  H2O
• ??????????????????????????????
• A peptide linkage (amide group)
• There are 20 amino acids commonly found in
  proteins.
• Additional condensation reaction produces
• polypeptide eventually yielding a protein

Dipeptide
128
The 20 Alpha-amino Acids found in most proteins
129
Levels of Structure

• Primary Sequence of amino acids in the protein
  chain. (lycine-alanine-leucne (lys-ala-leu).
• So many arrangements can be predicted.

Tripeptide containing Glycine, Cysteine, and
Alanine
130
Levels of Structure

• Secondary The arrangement of the protein chain
  in the long molecule (hydrogen bonding determines
  this).
• Hydrogen bonding between lone pairs on an oxygen
  atom in the carbonyl group of an amino acid and a
  hydrogen atom attached to a nitrogen of another
  amino acid

This type of interaction can occur with the chain
coils to form a spiral structure called ?- helix
131
Hydrogen bonding within a protein chain causes it
to form a stable helical structure called the
alpha-Helix
This is found in fibrous protein like wool and
hair giving it the elasticity
132

• Tertiary The overall shape of the protein
  (determined by hydrogen-bonding, dipole-dipole
  interactions, ionic bonds, covalent bonds and
  London forces).

Summary of the Various Types of Interactions that
Stabilize the Tertiary Structure of a Protein
(a) Ionic, (b) Hydrogen Bonding, (c) Covalent,
(d) London Dispersion, and (e) Dipole-Dipole
133
Summary of the Various Types of Interactions that
Stabilize the Tertiary Structure of a Protein
(a) Ionic, (b) Hydrogen Bonding, (c) Covalent,
(d) London Dispersion, and(e) Dipole-Dipole
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Carbohydrates

• Food source for most organisms and
• structural material for plants.
• Empirical formula (CH2O)n
• Most carbohydrates such as starch and cellulose
  are polymers of monosacharides or simple sugar
  monomers
• Monosaccharides (simple sugars) are
• polyhydroxy ketones and aldehydes
• Pentoses (5-carbon atoms) - ribose, arabinose
• Hexoses (6-carbon atoms) - fructose, glucose

135
Some Important Monosaccharides
136
Chiral carbon atoms in fructose

• Molecules with nonsuperimposable mirror images
  exhibit optical isomerism
• A carbon atom with different groups bonded to it
  in a tetrahedral arrangement always has a
  nonsuperimposable mirror images which gives rise
  to a pair of optical isomers

137
Tetrahedral Carbon atom with four different
substituents cannot have its mirror image
superimposed
138
The Mirror Image Optical Isomers of Glyceraldehyde
Chiral carbon atom

139
Fructose

There are 3 chiral Carbon atoms There are 23
isomers That differ in the ability To rotate light


140
Complex carbohydrates

• Disaccharides (formed from 2 monosaccharides
  joined by a glycoside linkage)
• sucrose (glucose fructose)
• Polysaccharides (many monosaccharide units)
• starch, cellulose

141
Sucrose is a disaccharideformed from
alpha-D-glucose and fructose
142
(a) The Polymer Amylose is a Major Component of
Starch and is Made Up of Alpha-D-Glucose
Monomers (b) The Polymer Cellulose, which
Consists of Beta-D-Glucose Monomers
143
Nucleic Acids

• Life is possible because each cell when it
  divides can transmit the vital information about
  how it works to the next generation
• The substance that stores and transmits
  information is a polymer called deoxyribonucleic
  acid (DNA)
• DNA together with other similar nucleic acids
  called ribonucleic acids is responsible for the
  synthesis of various proteins needed by the cell
  to carry out its life functions

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Nucleic Acids

• DNA (deoxyribonucleic acids) stores and
  transmits genetic information, responsible (with
  RNA) for protein synthesis. (Molar mass several
  billion)
• RNA (ribonucleic acid) helps in protein
  synthesis. (Molecular weight 20,000 to 40,000)

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Monomers of nucleic acidNucleotides

• 1. Five-carbon sugar, deoxyribose in DNA and
  ribose in RNA.
• 2. Nitrogen containing organic base
• 3. Phosphoric acid molecule, H3PO4

• The base and the sugar combine to form a unit
• that in turn reacts with phosphoric acid to
• create a nucleotide
• The nucleotides become connected through
  condensation reaction that eliminate water to
  give a polymer that contain a billion units.

146
The Organic Bases Found in DNA and RNA
147
The base and sugar combine to form a unit that in
turn reacts with phosphoric acid to create the
nucleotide, which is an ester
148
A Portion of a typical nucleic acid chain
149
Double helix formation

• According to Watson and Crick (Nobel prize
  winners), CAN is composed of two strands
  (threads) running in opposite directions that are
  bridged by hydrogen bonds between specific
  pyrimidine groups on one strand and purine group
  on the other
• The two strands are twisted into a double ?-helix
  structure
• The strongest hydrogen bonds form between adonine
  and thymine and between guanine and cystosine.
  Thus A-T or G-C bonding interactions will take
  place
• The sequence of nucleotides on one strand of the
  double helix determines the sequence of the other
• The sequence of the bases determines what
  information is stored.

150
(a) The DNA double helix contains two
sugar-phosphate backbones, with the bases from
the two strands hydrogen bonded to each other
the complementarity of the (b) thymine-adenine
and (c) cytosine-guanine pairs
151
Genetic Code and Protein Synthesis
follows!!!!!!!!!!!