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Title: Whenever we cook food, we are acting as organic chemists. The proteins, fats, and carbohydrates that make up our food are organic compounds, and cooking the food causes chemical reactions to occur that decompose some of the compounds into tastier ones.


1
Chapter 11. Carbon-Based Materials
  • Whenever we cook food, we are acting as organic
    chemists. The proteins, fats, and carbohydrates
    that make up our food are organic compounds, and
    cooking the food causes chemical reactions to
    occur that decompose some of the compounds into
    tastier ones. In this chapter we see a little of
    the amazing variety of organic compounds and
    study some of their reactions.

2
Assignment for Chapter 11
11.32 11.40 11.46 11.57 11.67 11.73 11.77
11.78 11.8711.92 11.93
3
Hydrocarbons and Functional Groups
  • Alkanes
  • Alkenes and Alkynes
  • Aromatic compounds
  • Functional Groups
  • Alcohols
  • Ethers
  • Phenols
  • Aldehydes and Ketones
  • Carboxylic Acids and Esters
  • Amines and Amides

4
Examples
Abbreviated structural formula
Structural formula
Name
(ordinary) molecular formula
5
????
6
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7
The molecule that shocked science more than once.
Friedrich August von Stradonitz Kekulé
(1829-1896) who proposed the ring model of
benzene in 1861
8
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????(????)
18
(???)
????
19
Alkanes saturated hydrocarbons
20
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21
Cycloalkanes
22
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Figure 11.1 The melting and boiling points of the
unbranched alkanes from CH4 to C16H34.
The dominant intermolecular force in alkanes is
the London force because they are nonpolar.
Melting point of propane (-187 oC) is lower than
that methane (-183 oC) and that of ethane(-172
oC) because of symmetry of methane is higher
than that of propane. As the number of carbons
increases, the symmetry contribution becomes less
and less significant. This initial glitch (the
anomalous increase of melting point of methane
and ethane), therefore, is because of the high
symmetry of the two molecules, which provides
extra, entropic contribution to enthalpy of
melting.
Obviously, there is no symmetry contribution to
boiling point.
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Straight Chain
26
Branched (with side chains)
27
Figure 11.2 (a) The atoms in neighboring
straight-chain alkanes, represented by the
tubelike structures, can lie close together. (b)
Fewer of the atoms of neighboring branched alkane
molecules can get so close together, so the
London forces (represented by double-headed
arrows) are weaker and branched alkanes are more
volatile.
28
Figure 11.3 The enthalpy changes accompanying the
combustion of methane. Although the bonds in the
reactants are strong, they are even stronger in
the products and the overall process is
exothermic.
29
Figure 11.4 In an alkane substitution reaction,
an incoming atom or group of atoms (represented
by the orange sphere) replaces a hydrogen atom in
the alkane molecule.
30
Alkenes and Alkynes
31
Figure 11.5 The ?-bond (yellow electron clouds)
in an alkene molecule makes the molecule
resistant to twisting around a double bond, so
all six atoms lie in the same plane.
32
Figure 11.6 The melting point of an alkene is
usually lower than that of the alkane with the
same number of carbon atoms. The values shown are
for unbranched alkanes and 1-alkenes (that is,
alkenes in which the double bond is at the end of
the carbon chain).
33
Figure 11.7 In an elimination reaction, two
atoms (the orange and purple spheres) attached to
neighboring carbon atoms are removed from the
molecule, leaving a double bond in their place.
34
Figure 11.8 In an addition reaction, the atoms
provided by an incoming molecule are attached to
the carbon atoms originally joined by a multiple
bond. Addition is the reverse of elimination.
35
Figure 11.9 When bromine dissolved in a solvent
(the brown liquid) is mixed with an alkene (the
colorless liquid), the bromine atoms add to the
molecule at the double bond, a reaction giving a
colorless product.
36
Aromatic Compounds (Arenes)
?
?
37
Schematic representation of coal
38
How to name hydrocarbons
  • Alkanes
  • (1) identify the longest unbranched chain and
    give it the name of the corresponding alkane.
  • (2)name the alkyl substituent groups by changing
    the suffix ane into yl. Use Greek prefix to
    indicate how many of each substituents are in the
    molecule. When different groups are present, list
    them in alphabetical order and attach them to the
    root name.
  • (3) Indicate the locations of the substituents by
    numbering the backbone carbone C atoms from
    whichever end of the molecule results in the
    lower numbers of locations for the substituents.
    The locations are then written before each
    substituent, separated by commas.

39
2,2,4-trimethylpentane
Except terminals, wherever there is a C or CH,
there is substituent(s).
Common mistakes 2-methyl-2-methyl-4-me
thylpentane 2-dimethyl-4-methylpentane
40
4,4,2-trimethylpentane
Using the smallest numbers possible.
41
How to name hydrocarbons
  • Alkenes and Alkynes
  • (1) identify the longest unbranched chain and
    give it the name of the corresponding alkene or
    alkyne.
  • (2)name the alkyl substituent groups by changing
    the suffix ane into yl. Use Greek prefix to
    indicate how many of each substituents are in the
    molecule. When different groups are present, list
    them in alphabetical order and attach them to the
    root name.
  • (3) Indicate the locations of the substituents by
    numbering the backbone carbon C atoms from
    whichever end of the molecule results in the
    lower numbers of locations for the substituents.
    The locations are then written before each
    substituent, separated by commas.
  • (4) Number the C atoms in the backbone in the
    order that gives the lower numbers to the two
    atoms joined by the multiple bond. The multiple
    bond has priority over the numbering of
    substituents.

42
Naming an Alkene
6 5 4 3 2 1
2-methyl-5-hexene
1 2 3 4 5 6
5-methyl-2-hexene
The multiple bond has priority over the numbering
of substituents
43
2,3-dimethyl-4-ethylcyclohexene
The multiple bond has priority over the numbering
of substituents (Use the smallest numbers to
locate the double bond)
CH2-CH3
CH3
CH3
44
2,3-dimethyl-4-ethylcyclohexene
1,6-dimethyl-5-ethylcyclohexene, 5-ethyl-1,6-dimet
hylcyclohexene, 1,2-dimethyl-3-ethylcyclohexene
45
How to name hydrocarbons
  • Arenes
  • -C6H5 aryl
  • ortho- (o-), meta (m-), para (p-)

1,4-dimethylbenzene (p-Xylene)
1,3-dimethylbenzene (m-Xylene)
1,2-dimethylbenzene (o-Xylene)
46
Exercise
  • Name the following hydrocarbons

(a) (CH3)2CHCH2CH(CH2CH3)2
1 2 3 4 5 6
(b)
(a) (CH3)2CHCH2CH(CH2CH3)2
  1. 4-ethyl-2-methylhexane
  2. 1-ethyl-3-propylbenzene

47
Quiz
  • Name and give an example of the major reactions
    of hydrocarbons.
  • Explain why the melting point and boiling point
    of a straight-chained hydrocarbon are higher than
    that a branched hydrocarbon of equal number of
    carbon atoms.
  • Draw the structures of
  • 4-ethyl-2-methylhexane,
  • 1-ethyl-3-propylbenzene
  • 5-methyl-2-hexene
  • Name the following compounds

48
Functional Groups
  • Alcohols
  • Ethers
  • Phenols
  • Aldehydes and Ketones
  • Carboxylic Acids and Esters
  • Amines and Amides

49
aa
50
Investigating Matter 11.1 (a) The two
orientations of a nuclear spin have the same
energy in the absence of a magnetic field. When a
field is applied, the energy of the ? spin falls
and that of the ? spin increases. When the
separation between the two energy levels is equal
to the energy of a radio-frequency photon, there
is a strong absorption of radiation, giving a
peak in the NMR spectrum.
Nuclear Magnetic Resonance
51
Investigating Matter 11.1 (b) The NMR spectrum of
ethanol. The red letters denote the protons that
give rise to the associated peaks.
The NMR spectrum of a molecule is like a
fingerprint.
52
Investigating Matter 11.1 (c) An MRI image of a
human brain. The patient must lie within the
strong magnetic field (background) and the
detectors can be rotated around the patients
head, which allows many different views to be
recorded.
Magnetic Resonance Imaging makes it possible to
see inside a sample noninvasively.
53
Alcohols
-OH
54
Ethers
R-O-R
Water, CH3CH2-O-H, CH3CH2-O-CH2CH3
55
Figure 11.12 The boiling points of ethers (given
on each column, in degrees Celsius) are lower
than those of isomeric alcohols, because hydrogen
bonding occurs in alcohols but not in ethers. All
the molecules referred to here are unbranched.
56
Phenols
57
????
(????)
58
????
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Aldehydes and Ketones
61
Smoked meat/fish
Wood smoke contains formaldehyde (formalin)
that has destructive effect on bacteria so smoked
food can be preserved long.
Simplest aldehyde HCHO
62
for aroma of cherries and almonds
63
In oil of cinnamon
64
in oil of vanilla
65
Major Properties
  • Aldehydes and ketones can be prepared by the
    oxidation of alcohols.
  • Aldehydes are reducing agents ketones are not.

66
Figure 11.13 An aldehyde (left) produces a
silver mirror with Tollens reagent, but a ketone
(right) does not.
67
Carboxylic Acids and Esters
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????
70
Figure 11.14 In a condensation reaction, two
molecules are linked as a result of removing two
atoms or groups of atoms (the orange and purple
spheres) as a small molecule (typically, water).
Carboxylic acid amine ?amide
water CH3COOHNH2CH3?CH3CONHCH3H2O
71
Amines and Amides
Amines derivatives from ammonia by replacing
hydrogens with organic
groups. Amides resulted from condensation of
amines with carboxylic acids.
Methylamine Dimethylamine Trimethylamine
Carboxylic acid amine ?amide
water CH3COOHNH2CH3?CH3CONHCH3H2O
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Naming Compounds with Functional Groups
  • Highlight functional groups. Numbering of carbons
    should results in lower number for the functional
    group.
  • Refer to conventions for hydrocarbons
  • Alcohols alkane?-ol CH3CH2CHOHCH3?2-butanol
  • Ethers Name each of hydrocarbon groups attached
    to the O atom separately and alphabetically.
    CH3OCH2CH3?ethyl methyl ether.
  • Aldehydes identify the parent alkane (including
    C of CHO in count of carbon atoms) change the
    final e into al. the CHO group can occur only
    at the end of a carbon chain and is given the
    number 1 only if other substituents need to be
    located. CH3CH(CHO)CH2CH3?2-methylbutanal.
  • Ketones Change the e in parent alkane into
    one. the CO group is indicated by selecting a
    numbering order that gives it the lower number.
    CH3CH2CH2COCH3?2-pentanone.
  • Carboxylic acidschange the e of the parent
    alkane into oic acid. Include the C atom of the
    COOH in count of carbon atoms.
    CH3CH2CH2COOH?butanoic acid.
  • Esters Change the ol of the alcohol to yl and
    the oic acid of the parent acid to oate.
    CH3CH2COOCH3?methyl propanoate.
  • Aminesspecify the groups attached to the
    nitrogen atom in alphabetical order, followed by
    the suffix amine. Amines with two amino acids
    are called diamines. The NH2 group is called
    amino- when it is a substituent.
    (CH3CH2)2NCH3?diethylmethylamine.
  • Halides Name the halogen atom as a substituent
    by changing the ine part of aits name to o.
    CH3Br?bromomethane.

75
Naming the following compounds
  1. CH3CH(CH3)CHOHCH3
  2. CH3CH2CH2COCH3
  3. (CH3CH2)2NCH2CH2CH3

(a) 3-methyl-2-butanol
(b) 2-pentanone
(c) diethylpropylamine
76
Exercise
  • Naming the following compounds
  • CH3CH(CH2CH2OH)CH3
  • CH3CH(CHO)CH2CH3
  • (C6H5)3N
  1. 3-methyl-1-butanol
  2. 2-methylbutanal
  3. triphenylamine

77
Classroom Exercise
  • Naming the following compounds
  • CH3CH2CHOHCH2CH3
  • CH3CH2COCH2CH3
  • CH3CH2NHCH3
  1. 3-pentanol
  2. 3-pentanone
  3. ethylmethylamine

78
Quiz
1. Name the following compounds
CH3CH2COOCH3
CH3CH2NHCH3
CH3CH2CH2COOH
2. What is most important difference between
aldelhyde and ketone?
3. Name the following reaction
CH3COOHNH2CH3?CH3CONHCH3H2O
79
Answer
1. Name the following compounds
3-methyl-1-butanol
2-methylbutanal
CH3CH2COOCH3
CH3CH2NHCH3
CH3CH2CH2COOH
methyl propanoate
butanoic acid
ethylmethylamine
2. What is most important difference between an
aldelhyde and a ketone?
An aldelhyde is a good reducing agent, but a
ketone is not.
3. Name the following reaction
CH3COOHNH2CH3?CH3CONHCH3H2O
Condensation reaction
80
Isomers
  • Structural isomers
  • Stereoisomers
  • Geometrical isomers
  • Optical isomers

81
Figure 11.15 A summary of the various types of
isomerism that occur in molecular compounds.
Geometrical and optical isomers are both types of
stereoisomers.
82
Structural Isomers C4H10
CH3-CH2-CH2-CH3
CH(CH3)3
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Structural Isomers C6H14
87
Isomer vs Conformation
They are the same isomer but with different
conformations
88
Exercise Different Isomers or Different
Conformers
89
Stereoisomerism IGeometric Isomerism
90
Figure 11.16 A pair of geometrical isomers in
which two groups are either both on the same side
of a double bond (cis) or on opposite sides
(trans). Notice that the bonded neighbors of each
atom are the same in both cases, but nevertheless
the arrangements of the atoms in space are
different.
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cis or trans?
(a) trans (b) cis
93
Classroom Exercise cis or trans?
(a) cis (b) trans
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Figure 11.17 Compounds with rings can also
exhibit geometrical isomerism. Groups attached to
carbon atoms in a ring can be both on the same
face of the ring (cis) or across the plane of the
ring from each other (trans).
96
the trans isomer has the higher melting
point the cis isomer has the higher boiling
point.
1,2-dichloroethene
isomer melting point (C) boiling point (C)
cis -80 60
trans -50 48
isomer melting point (C) boiling point (C)
cis-but-2-ene -139 4
trans-but-2-ene -106 1
Why is the boiling point of the cis isomers
higher? There must be stronger intermolecular
forces between the molecules of the cis isomers
than between trans isomers.
Why is the melting point of the cis isomers
lower? You might have thought that the same
argument would lead to a higher melting point
for cis isomers as well, but there is another
important factor operating. In order for the
intermolecular forces to work well, the molecules
must be able to pack together efficiently in the
solid. Trans isomers pack better than cis
isomers. The "U" shape of the cis isomer doesn't
pack as well as the straighter shape of the
trans isomer. The poorer packing in the cis
isomers means that the intermolecular forces
aren't as effective as they should be and so
less energy is needed to melt the molecule - a
lower melting point.
97
Stereoisomerism IIChirality (Enantiomerism)
98
Figure 11.18 The molecule on the right is the
mirror image of the molecule on the left, as can
be seen more clearly by inspecting the simplified
representations in the circles. Because the two
molecules cannot be superimposed, they are
distinct optical isomers.
99
All enantiomers have a stereogenic center
carbon. This makes the molecule chiral having a
non-superimposable mirror image. When we name
these enantiomers it is necessary to distinguish
them from one another. As it turns out each
enantiomer in the pair has opposite
configuration. Configuration is the
arrangement of the groups attached to a
stereogenic center. In one enantiomer the
arrangement is clockwise around the stereogenic
carbon beginning with the highest priority atom
or group. This is called the "R" configuration.
The letter "R" comes from the Latin Rectus
meaning right. The other enantiomer of the pair
being the non-superimposable mirror image will
always have an arrangement that proceeds counter
clockwise around the stereogenic carbon. This is
a different configuration and is called the "S"
isomer. The letter "S" comes from the Latin
Sinister meaning left. Now if we were to name the
two enantiomers using the systematic IUPAC
nomenclature system, they would have the same
name. We then attach at the beginning of the
name the letter "R" or "S" in parenthesis
100
ExerciseStructural isomers? Geometric isomers?
Or optical isomers? Conformers
101
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Figure 11.19 Plane-polarized light consists of
radiation in which all the wave motion lies in
one plane (as represented by the orange arrows on
the left). When such light passes through a
solution of an optically active substance, the
plane of the polarization is rotated through a
characteristic angle that depends on the
concentration of the solution and the length of
the path through it.
103
Figure 11.20 This polarimeter measures the
optical activity of compounds in solution. Light
is plane polarized by passage through a polarizer
and is then sent through a sample. An analyzer on
the right of the sample is rotated until the
angle at which the light is brightest is found.
That angle is the angle of rotation for the
sample.
104
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105
Predicting whether a molecule is chiral
Yes
106
Classroom Exercise Chiral?
CH3
CH3
CH3
CH3
No
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108
Example The significance of isomerism drug
efficiency
109
Quiz
  • Explain the differences in the melting point and
    boiling point of trans- and cis- isomers.
  • Are the following molecules chiral?

110
Polymers (macromolecules)
  • Synthetic polymers
  • Biopolymers (DNA, RNA, Carbohydrates, Proteins)

Homogenous polymer
Heterogeneous polymer
111
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Tacticity (stereoregularity)
114
Figure 11.21 The stereoregular polymers produced
by using Ziegler-Natta catalysts may be (a)
isotactic (all on one side) or (b) syndiotactic
(alternating). (c) In an atactic polymer, the
substituents lie on random sides of the chain.
115
Case Study 11This flexible polyacetylene sheet
was peeled from the walls of the reaction flask
in which it was made from acetylene.
116
Figure 11.22 Collecting latex from a rubber tree
in Malaysia, one of its principal producers.
117
Figure 11.23 In natural rubber, the isoprene
units are polymerized to be all cis. The harder
material, gutta-percha, is the all-trans polymer.
118
Condensation PolymerizationHow polymers are
synthesized
119
Example Synthesis of Dacron (Terylene)

120
Figure 11.24 Synthetic fibers are made by
extruding liquid polymer from small holes in an
industrial version of the spiders spinneret.
121
Figure 11.25 A scanning electron micrograph of
Dacron polyester and cotton fibers in a blended
shirt fabric. The cotton fibers have been colored
green. Compare the smooth cylinders of the
polyester with the irregular surface of cotton.
The smooth polyester fibers resist wrinkles, and
the irregular cotton fibers produce a more
comfortable and absorbent texture.
122
Figure 11.26 A rather crude nylon fiber can be
made by dissolving the salt of the amine in water
and dissolving the acid in a layer of hexane,
which floats on the water. The polymer forms at
the interface of the two layers, and a long
string can be slowly pulled out.
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PLAYING AROUND PRODUCES WONDER FIBER--NYLON A
team of organic chemists from Du Pont led by
Wallace Hume Carothers had been trying to unravel
the composition of natural polymers, such as
cellulose, silk, and rubber. From this knowledge
they hoped to develop synthetic materials that
mimicked the properties of these natural
polymers. This remarkable group of chemists had
developed a group of compounds, polyamides, which
had no remarkable or useful properties. These
compounds were shelved in order to concentrate
their work on a more promising series of
compounds, polyesters. Polyesters possessed more
desirable properties such as having more soluble
products, easier to handle and simpler to work
with in the laboratory. Julian Hill, working with
polyester, noticed that if you gathered a small
amount of this soft polymer on the end of your
stirring rod and drew it out of the beaker, it
produced a silky, fine fiber. One afternoon when
their boss, Wallace Carothers, was not in the
lab, the chemists decided to see how long a silky
thread they could produce. Hill and his cohorts
took a little ball on a stirring rod and ran down
the hall and stretched them out into a string.
The realization struck them during this
horseplay that by stretching the strand of fiber
they were orienting the polymer molecules and
increasing the strength of the product. The
polyesters had very low melting points, too low
for textile uses, so they retrieved the
polyamides from the shelf and began to experiment
with this need 'cold-drawing process.' They
found that the strand of polyamide produced by
this cold-drawing technique produced a stron g,
excellent fiber. The patent for the composition
of nylon was never applied for by Du Pont, rather
they chose to patent the production process --
cold-drawing -- developed by unsupervised adults
playing around in the lab. In January-February
1939, this consumer product hit the US market. It
is without equal in its impact before or since.
Nylon stockings were exhibited at the Golden
Gate International Exposition in San Francisco
and were sold first to employees of the inventor
company Du Pont de Nemours. On May 15, 1940,
nylon stockings went on sale throughout the US,
and in New York City alone four million pairs
were sold in a matter of hours. Naming this new
polymer too many twists and turns. Initially the
name norun was proposed for this new product
because it was more resistant to laddering than
silk. But there were problems and the name was
then reversed to read nuron. However, it was
pointed out that this was too close to the word
neuron which may be construed to be a nerve
tonic. Hence, nuron was changed nulon. However
this ran into trade mark problems and the name
was again changed to nilon. English speakers
differed in their pronunciation of this, so, to
remove ambiguity the name finally became nylon.
Two years before the basic patent on nylon had
been filed, the discoverer of nylon, Wallace Hume
Carothers, suffering from one of his increasingly
frequent attacks of depression, caused by his
conviction that he was a scientific failure,
drank juice containing potassium cyanide. He
would be pleased to know that half of all the
chemists in the US work on the preparation,
characterization, or application of polymers.
125
Figure 11.27 The strength of nylon fibers is yet
another sign of the presence of hydrogen bonds,
this time between neighboring polyamide chains.
126
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127
Figure 11.28 The two samples of polyethylene in
the test tube were produced by different
processes. The floating, low-density polymer was
produced by high-pressure polymerization. The
high-density polymer at the bottom was produced
with a Ziegler-Natta catalyst. As the insets
show, the higher density results from the greater
linearity of the chains, allowing them to pack
together better.
128
Figure 11.29 Automobile tires are made of
vulcanized rubber and a number of additives,
including carbon. The gray cylinders in the small
inset represent polyisoprene molecules, and the
beaded yellow strings represent disulfide (SS)
links that are introduced when the rubber is
vulcanized, that is, heated with sulfur. These
cross-links increase the resilience of the
treated rubber and make it more useful than
natural rubber.
129
Figure 11.30 This high-performance race car is
made of a composite material that is stronger
than steel and can withstand great stress.
130
Biopolymers
  • Proteins (polypeptides/polyamino acids)
  • Carbohydrates (polysaccharides)
  • DNA and RNA (Polynucleotides)

They are all heterogeneous polymers DNA/RNA
are four-letter sequences Proteins are
20-letter sequences Carbohydrates are
many-letter sequences
131
Proteins
  • Polymers formed by 20 different residues
  • of amino acids.

132
K R H W N Q P
G A F V L I S T Y D E C M
133
Non-polar Amino Acids
  • There are 8 non-polar amino acids

3D structures
134
Polar, Uncharged Amino Acids
  • There 7 polar, uncharged amino acids

3D structures
135
Polar, Charged Amino Acids
  • There are 5 polar charged amino acids

3D structures
136
Amino Acids not found in Proteins
  • Certain amino acids and their derivatives are
    biochemically important. For example, the visible
    symptoms of allergies are caused by the release
    of histamine in mast cells, a type of cell found
    in loose connective tissue. Histamine dilates
    blood vessels, increases the permeability of
    capillaries (allowing antibodies to pass from the
    capillaries to surrounding tissue), and
    constricts bronchial air passages. The molecular
    mechanism of histamine function is by its
    specific binding to a protein called histamine H1
    receptor.
  • Serotonin, which is derived from tryptophan,
    function as neurotransmitters and regulators.

137
Optical Activity and Stereochemistry of Amino
Acids
  • All amino Acids but glycine are chiral molecules.
    There are two possible configurations around Ca
    that constitute two non-superimposable mirror
    image isomers, or enantiomers. Enantiomers
    display optical activity in rotating the plane of
    polarized light. All natural amino acids are L-
    isomers.

138
Structure of peptide bond
  • Two amino acids are joined by the peptide bond, a
    reaction catalyzed by the enzyme called ribosome
    in all cells
  • Due to the double bond character, the six atoms
    of the peptide bond group are always planar.

139
The Level of Protein Structure
  • Primary Structrue (1º) refers to the amino acid
    sequences of proteins
  • Secondary Structure (2º) refers to segments that
    constitute structural conformities, or regular
    structures in proteins
  • Tertiary Structure (3º) refers to the folding of
    protein chains into a more compact three
    dimensional shape
  • Quaternary Structure (4º) refers to organization
    of subunits (one subunit is a single polypeptide
    chain).

140
Figure 11.31 A representation of part of an a
helix, one of the secondary structures adopted by
polypeptide chains. The tubes represent the atoms
and their bonds, with colors that correspond to
the colors commonly used to represent different
atoms. The narrow lines indicate hydrogen bonds.
The methyl group side chains show that this
molecule is polyalanine.
Example LSPADKTNVK VKGWAA STVLTSKLYR
141
Figure 11.32 One of the four polypeptide chains
that make up the human hemoglobin molecule. Each
chain consists of alternating regions of ? helix
(represented by red ribbons) and ?-pleated sheet.
The oxygen molecules we inhale attach to the iron
atom (blue sphere) and are carried through the
bloodstream to be released where they are needed.
142
Restriction by Amide Plane
  • Atoms in the peptide bond lie in a plane.
    Resonance stabilization energy of this planar
    structure is approximately 88 kJ/mol
  • Rotation can only occur around the two bonds
    connected to the Ca atom
  • Rotation around the Ca and carbonyl bond is
    called y (psi)
  • Rotation around the Ca and nitrogen bond is
    called f (phi).

143
Rotation of Amide Planes
  • If (f,y) are known for all residues, the
    structure for the entire backbone is known.
  • Some (f,y) are more likely than
  • others in a folded protein
  • Positive (f,y) values correspond
  • to clockwise rotation around bonds
  • when viewed from the Ca. Zero
  • is defined when the CO or N-H
  • bond bisects the R-Ca-H angle.
  • (f,y)(0,180), two carbonyl oxygens are too
    close
  • (f,y)(180,0), two amide groups are overlapping
  • (f,y)(0,0), carbonyl oxygen overlaps with amide
    group

144
Classes of Secondary Structures
  • Terms below define all classes of secondary
    structures seen in proteins
  • Helix
  • a-helix
  • 310 helix
  • Beta Sheet
  • Parallel
  • Anti-parallel
  • Beta-bulge
  • Beta Turn

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The Alpha Helix
  • The alpha helix is a helical structure. All alpha
    helices in proteins are right-handed
  • H-bond patterns of the alpha helix
  • Alpha helix Carbonyl oxygen of the ith residue
    forms H-bond with amide proton of the (i4)th
    residue. So there are n-4 H-bonds in a helix of n
    amino acids
  • 310 helix carbonyl oxygen of the ith residue
    forms H-bond with amide proton of the (i3)th
    residue. 3 residues (or 10 atoms) per turn
  • Proline is not found in a-helix except at the
    beginning of an a-helix
  • Helix propensity of an amino acid is a measure of
    the likelyhood for the amino acid to be in a
    helix Glu, Met, Ala, Leu have high propensities
  • Examples of a-helical proteins include a-keratin
    (structural proteins) and collagen (fibrous
    protein)
  • Linus Pauling (Nobel Prize in Chemistry, 1954)
    figured out the structure of a-keratin helix.

146
The Alpha Helix
  • Residues per turn 3.6
  • Rise per residue 1.5 Å
  • Rise per turn 5.4 Å
  • (f,y)(-60º,-45º)
  • CO N-H side chain
  • Total dipole moment

Showing dipole moments
147
The Beta Strands
  • Beta strands form beta sheet in proteins
  • H-bond patterns in beta strands
  • Parallel beta-strands (0.325 nm between two
    residues)
  • Anti-parallel beta-strands (0.347 nm between two
    residues)

148
The Beta Sheets
  • Formed by beta strands. Note that side chains
    point away from the sheet while main chains lie
    on the sheet. Sheets are the most extended form.
  • Sheets consist of parallel strands are usually
    larger that those consist of anti-parallel
    strands.
  • A sheet consists of parallel strands distribute
    hydrophobic residues on both sides of the sheet
    while that consist of antiparallel strands
    distributes hydrophobic residues on one side.

149
The Beta Turn (tight turn, or b-bend)
  • Beta turns connect beta strands and reverse the
    direction of beta strands
  • Proline and glycine have high propensity for beta
    turns
  • The carbonyl oxygen of the ith residue forms
    H-bond with the amide proton of the (i3)th
    residue
  • Tight turn promotes formation of antiparallel
    beta sheets.

150
The Beta Bulge
  • Beta bulge occurs between normal b-strands.
    Comprised of two residues on one strand and one
    on the other
  • Bulges cause bending of otherwise straight
    anti-parallel beta strands

Anti-parallel strands
Beta bulge
151
Super secondary Structures (I)
  • Hairpins connect two antiparallel strands
  • Cross-overs connect two parallel beta strands,
    most common through an a-helix (b-a-b topology).
    All cross-overs are right-handed. That is, when
    placing C-side strand closer and pointing right,
    the connecting a-helix or loop is on the top of
    the sheet

Right-handed Cross-over
Left-handed Cross-over
152
Super Secondary Structures (II)
  • Coiled-coil is a common alpha helix structure
    found in proteins that participate in protein
    folding and protein-protein interactions.
  • (a-b-c-d-e-f-g)n, where a and d are
  • nonpolar that leads to a hydrophobic side
  • Helix bundles refers to three or more helices
    packing together
  • Knobs into holes packing
  • In both kinds of helix packings, slight
    distortion
  • of the individual helices and the
  • inclination of their axes with respect
  • to each other allows the side chains
  • of the nonpolar residues to mesh together

153
Figure 11.33 The sickle-shaped red blood cells
that form when a certain glutamic acid residue in
hemoglobin (see Fig. 11.32) is replaced by valine.
154
Figure 11.34 The protein made by spiders to
produce a web is a form of silk that can be
exceptionally strong.
155
Figure 11.35 The thread on these spools is
synthetic spider silk, one of the strongest
fibers known. It can be used as the thin, tough
thread shown here or wound into cables strong
enough to support suspension bridges.
156
Carbohydrates
  • Carbohydrates are the most abundant organic
    molecules in nature
  • Photosynthesis energy stored in carbohydrates
  • Carbohydrates are the metabolic precursors of all
    other biomolecules
  • Important component of cell structures
  • Important function in cell-cell recognition
  • Carbohydrate chemistry
  • Contains at least one asymmetric carbon center
  • Favorable cyclic structures
  • Able to form polymers

157
Carbohydrate Nomenclature (I)
  • Carbohydrate Classes
  • Monosaccharides (CH2O)n
  • Simple sugars, can not be broken down further
  • Oligosaccharides
  • Few simple sugars (2-6).
  • Polysaccharides
  • Polymers of monosaccharides

158
Carbohydrate Nomenclature (II)
  • Monosaccharide (carbon numbers 3-7)
  • Aldoses
  • Contain aldrhyde
  • Name aldo--oses (e.g., aldohexoses)
  • Memorize all aldoses in Figure ?
  • Ketoses
  • Contain ketones
  • Name keto--oses (ketohexoses)

159
Polysacchrides
  • Also called glycans
  • Starch and glycogen are storage molecules
  • Chitin and cellulose are structural molecules
  • Cell surface polysaccharides are recognition
    molecules.

160
Figure 11.36 The amylose molecule, one component
of starch, is a polysaccharide. A polymer of
glucose, it consists of glucose units linked
together to give a structure like this but with a
moderate degree of branching.
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Polysacchrides
  • Glucose is the monosaccharides of the following
    polysacchrides with different linkages and
    banches
  • a(1,4), starch (more branch)
  • a(1,4), glycogen (less branch)
  • a(1,6), dextran (chromatography resins)
  • b(1,4), cellulose (cell walls of all plants)
  • b(1,4), Chitin similar to cellulose, but C2-OH is
    replaced by NHCOCH3 (found in exoskeletons of
    crustaceans, insects, spiders)

164
Figure 11.37 The amylopectin molecule is another
component of starch. It has a more highly
branched structure than amylose.
165
Figure 11.38 (a) Cellulose is yet another
polysaccharide constructed from glucose units.
The linking between the units in cellulose
results in long, flat ribbons that can produce a
fibrous material through hydrogen bonding. (b)
These long tubes of cellulose formed the
structural material of an aspen tree.
166
DNA and RNA
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A
170
G
171
C
172
T
173
U (in RNA)
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Extension of the DNA chain
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Figure 11.41 The condensation of nucleotides that
leads to the formation of a nucleic acida
polynucleotide. The lens-shaped object is an
attached amine.
178
Figure 11.42 The bases in the DNA double helix
fit together by virtue of the hydrogen bonds that
they can form as shown on the left. Once formed,
the AT and GC pairs are almost identical in size
and shape. As a result, the turns of the helix
shown on the right are regular and consistent.
179
Figure 11.39 A computer graphics image of a short
section of a DNA molecule, which consists of two
entwined helices. In this illustration, the
double helix is also coiled around itself in a
shape called a superhelix.
180
Figure 11.40 A DNA molecule is very large, even
in bacteria. In this micrograph, a DNA molecule
has spilled out through the damaged cell wall of
a bacterium.
181
The Code of Life
  • Three-letter code of DNA ? Amino acids?Proteins
  • ?All other molecules
  • ?Organism

182
Assignment for Chapter 11
11.32 11.40 11.46 11.57 11.67 11.73 11.77
11.78 11.8711.92 11.93
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