organic chemistry

1. By : Huda Eid Abdelwahab Nowar

2. 1. Introduction of carbohydrates
Carbohydrate is a organic compound. Carbohydrates are hydrates of
carbon, technically they are polyhydroxy aldehydes and ketones.
Carbohydrates are also known as saccharides, the word saccharide
comes from Greek word sakkron which means sugar. Polyhydroxy
aldehydes or ketones, or substances that yield such
compounds on hydrolysis.
• (CH2O)n
• 70-80% human energy needs
• >90% dry matter of plants

3. Properties of Carbohydrates
General properties of carbohydrates
Carbohydrates act as energy reserves, also stores fuels, and metabolic
intermediates.
Ribose and deoxyribose sugars forms the structural frame of the
genetic material, RNA and DNA.
Polysaccharides like cellulose are the structural elements in the cell
walls of bacteria and plants.
Carbohydrates are linked to proteins and lipids that play important
roles in cell interactions.
Carbohydrates are organic compounds, they are aldehydes or
ketones with many hydroxyl groups.

4. Physical Properties of Carbohydrate
 Steroisomerism – Compounds having same structural formula
but they differ in spatial configuration. Example: Glucose has two
isomers with respect to penultimate carbon atom. They are D-
glucose and L-glucose.
Optical Activity - It is the rotation of plane polarized light
forming (+) glucose and (-) glucose.
Diastereo isomers - It the configurational changes with regard
to C2, C3, or C4 in glucose. Example: Mannose, galactose.
Annomerism - It is the spatial configuration with respect to the
first carbon atom in aldoses and second carbon atom in ketoses.

5. 2. Stereochemistry and
Configuration

6. STEREOISOMERS
Compounds having same structural formula, but
differ in spatial configuration.
(Chiral center) Asymmetric Carbon atom:
Attached to four different atoms or groups.
Vant Hoff’s rule: The possible isomers (2n) of a
given compound is determined by the number
of asymmetric carbon atoms (n).
Reference C atom: Penultimate C atom, around
which mirror images are formed.

7. R,S System
 Suppose you had a model of one of these glucose
enantiomers in your hand. You could, of course, use
the R,S ( Prelog) system to describe the configuration
of one or more of the asymmetric carbon atoms.
7

8. Even though the R,S system is widely accepted today as a
standard for designating configuration, the configuration of
carbohydrates as well as those of amino acids and many other
compounds in biochemistry is commonly designated by the D,L
system proposed by Emil Fischer in 1891.
8
CHO
CH OH
CH2OH
CHO
C HHO
CH2OH
(R)-Glyceraldehyde (S)-Glyceraldehyde
4 C 3
1
2
4 C 2
1
3
(S) (R)

9. The D,L is ( Rosanoff) system
Dextrorotatory (+) :If sugar solution turns the plane of polarized light to right.
Levorotatory (–) :If the sugar solution turns the plane of polarized light to left.
Racemic mixture: Equimolar mixture of optical isomers has no net rotation.
1. Monosaccharides contain one or more asymmetric C-atoms: get D- and L-
forms, where D- and L- designate absolute configuration
2. D-form: -OH group is attached to the right of the asymmetric carbon
3. L-form: -OH group is attached to the left of the asymmetric carbon
4. If there is more than one chiral C-atom: absolute configuration of chiral C
furthest away from carbonyl group determines whether D- or L-
Optical activity
D and L configurations

10. examples of
chiral Carbon
atoms:
Highest
numbered
streocenter

11. The aldo hexoses have four asymmetric carbons
and therefore exist as 16 possible stereo isomers.

11
HOH2C
OH
H
C
OH
H
C
OH
H
C
H
C
OH
C
H
O
Aldohexoses
four asymmetric carbons
24
= 16 stereoisomers
1 2 3 4

12. Diastereomers
 Each diastereomer is a different carbohydrate with different
properties, known by a different name.
 Each of the monosaccharides has an enantiomer. For example,
the two enantiomers of glucose have the following structures:
12
HC
OHH
HHO
OHH
OHH
CH2OH
HC
HO H
H OH
HO H
HO H
CH2OH
O
Enantiomers of glucose
D - L -
O

13. EPIMERISM
Sugars are different from one another, only in configuration with
regard to a single C atom (other than the reference C atom).

14. Chemists commonly use two-dimensional representations
called Fischer projections to show the configuration of
carbohydrates.
A Fischer projection is used to differentiate between L-
and D- molecules. On a Fischer projection, the
penultimate carbon of D sugars are depicted with
hydrogen on the left and hydroxyl on the right. L sugars
will be shown with the hydrogen on the right and the
hydroxyl on the left.

15. Fischer Projection Formulas
(ACyclic Form of Carbohydrate)
Fischer Projection Formulas
(ACyclic Form of Carbohydrate)
 The Fischer projection, devised by Hermann Emil Fischer in 1891,
 is a two-dimensional representation of a three-dimensional organic
molecule by projection
15

16.  The horizontal segments of a Fischer projection represent
bonds directed toward the viewer (coming out of the plane of
the paper) and the vertical segments represent bonds directed
away from the viewer (going behind the plane of the paper) .
The only atom in the plane of the paper is the chiral center.
16
Paper plane

17. When relating one Fischer projection to another, it's
important to realise that it may only be manipulated
within the 2D plane in which it is drawn (that is, it
may not be rotated within 3D space), and even then,
it can only rotated in the plane it is drawn (2D) by 180o

18. Why can't you rotate it 270o
or 90o
?
A 90o
rotation is equivalent to breaking bonds and
exchanging two groups, which would result in the
formation of the other enantiomer.

19. Fischer proposed that these enantiomers be designated
D and L (for dextro and levorotatory) but he had no
experimental way to determine which enantiomer has
which specific rotation.
He assigned the dextrorotatory enantiomer an arbitrary
configuration and named it D-glyceraldehyde. He
named its enantiomer L-glyceraldehyde.
19
CHO
CH OH
CH2OH
D-Glyceraldehyde
[α]D = +13.5
CHO
C HHO
CH2OH
25
L-Glyceraldehyde
[α]D = -13.525

20.  Fischer could have been wrong, but it was proven in 1952 by
a special application of X-ray crystallography.
 D- and L-glyceraldehyde serve as reference points for the
assignment of relative configuration to all other aldoses and
ketoses.
The reference point is the chiral center farthest from the
carbonyl group. Because this chiral center is always the next
to the last carbon on the chain, it is called the penultimate
carbon.
 A D-monosaccharide has the same configuration at its
penultimate carbon as D-glyceraldehyde (its-OH is on the
right when written as a Fischer projection); an L-
monosaccharide has the same configuration at its penultimate
carbon as L-glyceraldehyde.
20

21. When creating a Fischer projection for a carbohydrate
with more than three carbons, each down carbon that
would project away from you as viewed from the top in
the Zig-Zag model must be turned around and oriented
as towards your view. However this does not alter the
Fischer projections for any previous carbons.
CHO
H OH
H OH
CH2OH
CHO
HO H
H OH
CH2OH
D-(-)-Erythrose D-(-)-Threose
CHO
H OH
H OH
H OH
CH2OH
D-(-)-Ribose
H
OH
O
OH
H2
C
HO
H
O
OH
H2
C
HO
OH
H
OH
O
OH
C
H2
OH
HO
4
3
2
15
2(R),3(R),4(R),5-tetrahydroxypentanal

22. Haworth Projection ( Cyclic Form)
Cyclization via intramolecular hemiacetal (hemiketal) formation
C-1 becomes chiral upon cyclization - anomeric carbon
Anomeric C contains -OH group which may be α or β
(mutarotation α ⇔ β)

23. The Haworth projection can be obtained from a Fischer projection in the
following way:
 The C5 hydrogen exchange with the C5 hydroxymethyl group of α-D-
glucopyranose written as Fischer projection will produce A .
 whereas the C5 hydrogen exchange with the C5 ring oxygen will produce B
Fischer A B Haworth

24. Haworth Projection

25. A ketose: Fructose α

26. In the Fischer projection, at the anomeric and the reference carbon atom is
designated α. In the α-anomer, the exocyclic oxygen atom at the anomeric center is
formally cis to the oxygen atom attached to the anomeric reference atom; in the β
anomer, these oxygen atoms are formally trans.

28. α
β
α
β

29. Conformation of a molecule can be defined as a spatial arrangement
of its atoms (or ligands) in a molecule that is obtained by free rotations
about single bonds.
The rotation of two methyl groups of ethane about the C–C single bond
should theoretically produce also an “infinite” number of
conformations if the rotation about the C–C bond was completely free.
However, due to a nonbonded interaction between the hydrogen atoms
on two adjacent methyl groups torsional or Pitzer strain ‫وتراجع‬ ‫تكتمل‬ ‫لم‬

30. Conformation of monosaccharide
Of furanose
form
Of pyranose
form

31. Conformational Analysis of Cyclic (Lactol,
Hemiacetal)Forms of Monosaccharides
Furanose ring structures occur in envelope
(E) and twist (T) conformations.
 As the difference in energy between the
different conformations on the wheel is generally
low, two regions having low energy
conformations occurring in the Northern and
Southern can be identified.

32. a pseudo-rotational wheel

33. Six-membered ring structures can occur in:
two chair (C), six boat (B), six skew (S), and twelve half-
chair ( H) conformations.
In practice, the two chair conformations have the lowest
energy, and strongly dominate.
The preference for these low energy conformations is
dictated by the relative orientations of the hydroxyl
groups. In the case of D-glucopyranoses, only the 4C1
conformation is of importance, whereas the 1C4
conformation dominates in α-D-idopyranose.
Cases occur as in β-D-arabinopyranose where both chair
conformations are in equilibrium.

35. 3. Carbohydrat
Classfication

36. There are three major size classes of
carbohydrates:
Monosaccharides
carbohydrates that cannot be hydrolyzed to simpler
carbohydrates; eg. Glucose or fructose.
Oligosaccharides
carbohydrates that can be hydrolyzed into a few (2-10)
monosaccharide units; eg. Sucrose or lactose
Polysaccharides
carbohydrates that are yield larg number of monosaccharide; eg
Starch or cellulose

37. Monosaccharide
Classified according to : (1)number of carbon atoms
(2) What they contain; an aldehyde or keto group

38. The structure and classification of some
monosaccharides

39. Nomenclature
Number of
carbons
Functional group
Ketone Aldehyde
4 Ketotetrose aldotetrose
5 Ketopentose Aldopentose
6 Ketohexose Aldohexose
7 ketoheptose aldoheptose

40. Reactions of Monosaccharides
I. Isomerization reaction
II. Addition reaction of carbonyl group
III. Nucleophilic substitution reaction of the anomeric
carbon
IV. Reactions of the hydroxyl group
V. Oxidation
VI. reduction

41. I. Isomerization reaction
A. Mutarotation (anomerization)

42. B. Epimerization

43. Hydride transfer mechanism:

44. II. Addition reaction of carbonyl group

45. B. Addition of nitroalkan

46. C. Addition of diazomethan

47. D. Wittig Reaction
Olefinic
sugar

48. E. Condensation with N,N-disubstituted hydrazine

49. F. Condensation with hydrazine

50. G. Condensation with aryl hydrazine ( osazone formation)

51. Due to the chelated structure of osazone

52. Saccharide arylosazone undergo some important
reactions :
1- Oxidative cyclization
2- Reductive elimenation

53. H. Condensation with hydroxyl amine

54. III. Nucleophilic substitution reaction of the anomeric
carbon
The two main reactions are:
(a) glycosidation
(b) glycosyl halide formation

55. A. Glycosidation
A leaving group (OH, OCOR, X) at the anomeric carbon is
displaced by an alkoxy (OR) or aryloxy (OAr) to give
glycofuranoside or glycopyranoside.

56. 1- Fischer glycosidation
Methyl glycoside
More stable

57. 2- Helferich glycosidation
Helferich glycosylation reaction has been used to
synthesize O-glycosides from protected glycosyl
bromide and alcohol (or another carbohydrate) in the
presence of mercuric cyanide. It is also referred to as
the Helferich condition. This reaction involves the SN2
substitution mechanism leads the formation of β-
glycoside and release of HgCNBr. This reaction has
been used in the preparation of glycosides.

58. 3- Koenigs-Knorr glycosidation
is the substitution reaction of a glycosyl halide with
an alcohol to give a glycoside

59. B. Glycoyl halide formation

60. GLYCOSIDE FORMATION
The hydroxyl group of anomeric carbon of a
carbohydrate can join with a hydroxyl group of another
carbohydrate or some other compound to form a
glycoside and the bond so formed is known as glycosidic
bond.
eg. R-OH + HO-R' 􀃆R-O-R' + H2O
The non-carbohydrate moiety is known as aglycone –
phenol, sterol, bases, CH3OH, glycerol.
Glycosidic bond can be N-linked or, O-linked.

62. IV. Reactions of the hydroxyl group
RCOOR’ ROR’

63. 1. Ester formation
Benzoyl chloride
Benzoate ester
Acetate ester
1- acetate ester
2- benzoate ester

64. Sulfonate ester
Intramolecular displacement
trans
α,β-anhydro sugar
(epoxy)
3- sulphonate ester

65. Displacement with OH-
Displacement with RCOO-
cis

66. 4- phosphate ester
5- sulfate ester

67. 2. Ether formation

70. 3. Cyclic acetal and ketal formation
RR

72. V. Oxidation and reduction
Oxidation Reduction
To aldonic by Br2 NaBH4
To aldaric by HNO3 LiAlH4

73. AMINO SUGARS
Amino groups are substituted for hydroxy groups
of sugars.

74. DEOXY SUGARS
Oxygen of the hydroxyl group is removed to form
deoxy sugars.
Non reducing and non osazone forming.
important part of nucleic acids.

75. Oligosaccharides
Composed of a few monosaccharide units by glycosidic
link from C-1 of one unit and -OH of second unit
1→3, 1→4, 1 → 6 links most common but 1 → 1 and 1
→ 2 are possible
Links may be α or β
Link around glycosidic bond is fixed but anomeric
forms on the other C-1 are still in equilibrium

76. Disaccharides
• Three main disaccharides: sucrose
maltose
lactose
• All are isomers with molecular formula C12H22O11
• On hydrolysis they yield 2 monosaccharide.
• which soluble in water
• Even though they are soluble in water, they are too
large to pass through the cell membrane.
76

77. Disaccharides

78. Sucrose
cane sugar
When hydrolyzed, it forms a mixture of glucose and
fructose
Dehydration synthesis of a sucrose molecule formed
from condensation of a glucose with a fructose
78

79. Formation of sucrose
79
α β

80. Maltose
 malt sugar.
Present in germinating grain.
Produced commercially by hydrolysis of starch.
80

81. Formation of maltose
81

82. Lactose
known as milk sugar.
Bacteria cause fermentation of lactose forming lactic
acid.
When these reaction occur ,it changes the taste to a
sour one.
82

83. Formation of lactose
83

84. Higher Oligosaccharides

86. Polysaccharid
es
Polysaccharide Animation.mp4

87. Polysaccharides are large molecules containing 10 or
more monosaccharide units.
Polysaccharides are complex carbohydrates made
uplinked monosaccharide units
monosaccharides or their derivatives held together
by glycosidic bonds.
Sources of Polysaccharides
Microbial fermentation
Higher plants
87
Polysaccharides

88. Poly
Saccharides

90. Poly
saccharides

91. storage
Polysaccharides

92. 1.Starch
Starch is a storage compound in
plants, and made of glucose units
It is a homopolysaccharide made up
of two components: amylose and
amylopectin.
Most starch is 10-30% amylose and
70-90% amylopectin

93. Amylose and amylopectin—starch
Starch is a mixture of amylose and amylopectin and is
found in plant foods.
Amylose makes up 20% of plant starch and is made
up of 250–4000 D-glucose units bonded α(1→4) in a
continuous chain.
Long chains of amylose tend to coil.
Amylopectin makes up 80% of plant starch and is
made up of D-glucose units connected by α(1→4)
glycosidic bonds.
93

94. 2. Amylose
 a straight chain structure formed by 1,4 glycosidic bonds
between α-D-glucose molecules.
H O
OH
H
OHH
OH
CH2OH
H
O H
H
OHH
OH
CH2OH
H
O
HH H O
O
H
OHH
OH
CH2OH
H
H H O
H
OHH
OH
CH2OH
H
OH
HH O
O
H
OHH
OH
CH2OH
H
O
H
1
6
5
4
3
1
2
amylose
Structure of Amylose Fraction of Starch

95. • The amylose chain forms a
helix.
• This causes the blue colour
change on reaction with
iodine.
• Amylose is poorly soluble in
water, but forms micellar
suspensions
Amylose

96. Amylopectin causes
a red-violet colour
change on reaction
with iodine.
This change is
usually masked by
the much darker
reaction of amylose
to iodine. Amylopectin
3. Amylopectin

97. Amylopectin-a glucose polymer with mainly α -(1→4)
linkages, but it also has branches formed by α -(1→6)
linkages. Branches are generally longer than shown above.
H O
OH
H
OHH
OH
CH2OH
H
O H
H
OHH
OH
CH2OH
H
O
HH H O
O
H
OHH
OH
CH2
H
H H O
H
OHH
OH
CH2OH
H
OH
HH O
O
H
OHH
OH
CH2OH
H
O
H
O
1 4
6
H O
H
OHH
OH
CH2OH
H
H H O
H
OHH
OH
CH2OH
H
H
O
1
OH
3
4
5
2
amylopectin
Structure of Amylopectin Fraction of Starch

98. Starch therefore consists of amylose helices entangled on
branches of amylopectin.

99. 4. Glycogen
Storage polysaccharide in animals
Glycogen constitutes up to 10% of liver mass and 1-2% of
muscle mass
Glycogen is stored energy for the organism
Similar in structure to amylopectin, only difference from starch:
number of branches
Alpha(1,6) branches every 8-12 residues
Like amylopectin, glycogen gives a red-violet color with iodine

100. Glycogen is a storage polysaccharide found in
animals.
Glycogen is stored in the liver and muscles.
Its structure is identical to amylopectin, except that
α(1→6) branching occurs about every
12glucose units.
When glucose is needed, glycogen is hydrolyzed in the
liver to glucose.
100

101. glycogen

102. structural
Polysaccharid
es

104. Cellulose
Cellulose contains glucose units bonded β(1→4).
This glycosidic bond configuration changes the three-
dimensional shape of cellulose compared with that of
amylose.
The chain of glucose units is straight. This allows
chains to align next to each other to form a strong rigid
structure.
104

105. The β-glucose molecules are joined by condensation, i.e. the removal
of water, forming β-(1,4) glycosidic linkages.
Note however that every second β -glucose molecule has to flip over to
allow the bond to form. This produces a “heads-tails-heads”
sequence.
The glucose units are linked into straight chains each 100-1000 units
long.
Weak hydrogen bonds form between parallel chains binding them
into cellulose microfibrils.
Cellulose microfibrils arrange themselves into thicker bundles called
microfibrils. (These are usually referred to as fibres.)
The cellulose fibres are often “glued” together by other compounds such
as hemicelluloses and calcium pectate to form complex structures such
as plant cell walls.

106. Cellulose is an insoluble fiber in our diet
because we lack the enzyme cellulase to
hydrolyze the β(1→4) glycosidic bond.
Whole grains are a good source of cellulose.
Cellulose is important in our diet because it
assists with digestive movement in the small
and large intestine.
Some animals and insects can digest cellulose
because they contain bacteria that produce
cellulase. 106

107. 107

110. 2. pectin
Cell wall
polysaccharide

111. • Source: Cell walls of higher plants (citrus rind)
• Structure: Largely a linear polymer of polygalacturonic acid with varying
degrees of methyl esterification. (Also some branches –HAIRY REGIONS)
– >50% esterified is a high methoxy (HM) pectin
– <50% esterified is a low methoxy (LM) pectin
• Functional Properties:
Main use as gelling agent (jams, jellies)
– dependent on degree of methylation
– high methoxyl pectins gel through H-bonding and in presence of sugar
and acid
– low methoxyl pectins gel in the presence of Ca2+
Thickeners
Water binders
Stabilizers

112. Pectin Model

113. 3. Chitin
Chitin makes up the exoskeleton of insects and
crustaceans and cell walls of some fungi.
It is made up of N-acetyl glucosamine
containing β(1→4) glycosidic bonds.
It is structurally strong.
Chitin is used as surgical thread that
biodegrades as a wound heals.
It serves as a protection from water in insects.
Chitin is also used to waterproof paper, and in
cosmetics and lotions to retain moisture.
113

114. 114

115. 4.Heparin
Heparin is a medically important polysaccharide
because it prevents clotting in the bloodstream.
115

116.  It is a highly ionic polysaccharide of repeating
disaccharide units of an oxidized monosaccharide
and D-glucosamine. Heparin also contains sulfate
groups that are negatively charged.
 It belongs to a group of polysaccharides called
glycosaminoglycans.

117. The major repeating unit is the trisulfated disaccharide
2-O-sulfo-α-L-iduronic acid 1"4 linked to 6-O-sulfo-N-
sulfo-α-D-glucosamine ("4]IdoA2S(1"4)GlcNS6S[1")

118. 5- chitosan
Source: Crustacean shells, insect exoskeleton and
some fungi = mainly chitin.
β(1 4) linked D-glucos-2-amine units

119. 119
Chitin
Chitosan
Deacetylation
(boiling 40-50%
NaOH)

120. 120

121. Other polysaccharidesOther polysaccharides
• CalloseCallose (poly 1-3 glucose), found in the walls of(poly 1-3 glucose), found in the walls of
phloem tubes.phloem tubes.
• DextranDextran (poly 1-2, 1-3 and 1-4 glucose), the storage(poly 1-2, 1-3 and 1-4 glucose), the storage
polysaccharide in fungi and bacteria.polysaccharide in fungi and bacteria.
• InulinInulin (poly fructose), a plant food store.(poly fructose), a plant food store.
• AgarAgar (poly galactose sulphate), found in algae(poly galactose sulphate), found in algae
and used to make agar plates.and used to make agar plates.
• MureinMurein (a sugar-peptide polymer), found in(a sugar-peptide polymer), found in
bacterial cell walls.bacterial cell walls.
• LigninLignin (a complex polymer), found in the walls of(a complex polymer), found in the walls of

123. (a) Flat ribbon type conformation: Cellulose
(b) Buckled ribbon type conformation: Alginate

124. 2- Hollow helix type structures
Tight helix - void can be filled by
including molecules of appropriate size
and shape
More extended helix - two or three
chains may twist around each other to
form double or triple helix
Very extended helix - chains can nest,
i.e., close pack without twisting around
each other
amylose-iodine helix

125. Amylose forms inclusion complexes with iodine, phenol,n-butanol, etc.

126. Examples of a single helix (cellulose), a double helix (amylose)
and a triple helix (β-1→3-glucan).

127. Conformation Zones
Zone A: Extra-rigid rod: schizophyllan
Zone B: Rigid Rod: xanthan
Zone C: Semi-flexible coil: pectin
Zone D: Random coil: dextran, pullulan
Zone E: Highly branched: amylopectin,
glycogen

128. PROTEOGLYCANS & GLYCOPROTEINS
Proteoglycans: When carbohydrate chains are
attached to a polypeptide chain.
Glycoproteins: Carbohydrate content ≤ 10%.
Mucoprotein: Carbohydrate content ≥10%

129. Four levels of Protein Structure
(a) The primary structure is the succession of amino acid
residues, usually abbreviated by the 1- or 3-letter codes.

130. (b) The secondary structure is the 3-D arrangement of the right-
handed alpha helix , or alternative structures such as a beta-
pleated sheet.

131. (c) The tertiary structure is the 3-D folding of the alpha helix
(show as a purple ribbon), shaped by structures such
as proline corners, disulfide
bridges between cysteine residues, and electrostic bonds.

132. (d) Where more than one protein chain contributes to the protein,
the quaternary structure is the arrangement of these subunits.
In hemoglobin as shown here, the quaternary structure comprises
two alpha and two beta polypeptides, held together by elecrostatic
bonds.

133. The Four Levels of Protein Structure.mp4

134. Monosaccharide component
The polysaccharide samples are hydrolyzed by
HCl/MeOH and TFA, then analyzed by HPLC or GC
HPLC:
High pressure/performance
liquid chromatography

135. Sugar linkage type
Chemical methods:
Periodate Oxidation and Smith degradation
Methylation analysis
GC-MS:
Gas chromatography-
Mass spectrometer

136. Physical methods:
NMR(Nuclear Magnetic Resonance)
• Sugar linkage type
• Monosaccharide configuration
• Substitute units
• Degree of branching

137. Physical methods:
FT-IR (Fourier transform infrared spectroscopy)
• Monosaccharide configuration
• Substitute units

138. Physical methods:
MS (Mass spectrometer)
• Sugar linkage type
• Monosaccharide configuration
• Substitute units
• Degree of branching
• Molecular weight