1. This document provides an overview of biochemistry for graduate study, covering the four main types of biomolecules - carbohydrates, lipids, nucleic acids, and proteins. 2. It describes carbohydrates in detail, explaining their monomer units, classifications, structures, properties and biological roles. This includes monosaccharides, oligosaccharides, polysaccharides, and glycoconjugates. 3. Key polysaccharides discussed are starch, glycogen, cellulose, chitin, glycosaminoglycans, and peptidoglycan. Glycoconjugates such as proteoglycans, glycolipids, and glycoproteins are also summarized.

1. BIOCHEMISTRY FOR GRADUATE STUDY I
318 701
1
Orientation: Course schedule
Assoc. Prof. Dr. Yanee Trongpanich

2. 2
Diverse living organisms share common chemical features

3. Biomolecules: The molecules of life
3
• All living organisms build molecules from the same kinds of
monomeric subunits.
• The structure of a macromolecule determines its specific
biological function.

4. 4
4 types of Biomolecules
 Carbohydrates
 Lipids
 Nucleic acid
 Amino acids and Protein

5. Carbohydrates
5
Learning Objective
o Define the carbohydrates, mono-, oligo- and polysaccharides
o Classify carbohydrate on the basis of their structures
o Explain glycosidic bond and the different structure of some
oligosaccharides
o Describe general characteristic of polysaccharides
o Appreciate the role of carbohydrates in biosystem
At the end of lecture students should be able to:

6. Carbohydrates
 Polyhydroxy aldehydes (-HC=O) or
ketones (-RC=O), or substances that
yield such compounds on hydrolysis.
 Some also contain nitrogen,
phosphorus, or sulfur.
 Empirical formula : (CH2O)n
starch grains (lightly stained
with iodine) in the cells of
the white potato
6

7. Carbohydrate roles
Wang's mannose-rich cluster molecule
resembles the target for an HIV-1 antibody 7
 served as fuels ; starch and glycogen
 served as structural and protective elements; cellulose, chitin
and peptidoglycan
 used as lubricate skeletal joints; glycosaminoglycan
 covalently attached to proteins or lipids act as signals and
participate in recognition and adhesion between cells;
glycoconjugates

8. Classes of carbohydrates
(Saccharide =sakcharon (Greek) = sugar)
1. Monosaccharides
2. Oligosaccharides
3. Polysaccharides
8

9. Monosaccharides
o a single polyhydroxy aldehyde or ketone unit
o Aldose : aldehyde group
Ketose : ketone group
o Empirical formula : (CH2O)n, n = 3+
9
o -ose suffix; aldose , ketose
o refer to the number of carbon atom; pentose,
hexose
o refer to the funtional group ; aldohexose,
ketopentose
o common name : fructose, sorbose
aldopentose : D-ribose ketopentose : D-ribulose
Monosaccharide Nomenclature

10. • Aldose and ketose can interconvert via an enediol intermediate.
• When the structures of molecules are related in these ways
(different in the position of the hydrogen and double bonds), the
molecules are called tautomers.
Triose : aldotriose (carbonyl group) ketotriose (ketone group)
10
D-glyceraldehyde Dihydroxyacetone
Enediol
intermediate

11. Properties of monosaccharides
• All monosaccharides except dihydroxyacetone contain one or more
asymmetric (chiral) carbon atoms and thus occur “stereoisomers”
• In general, a molecule with “n” chiral carbons can have 2n
stereoisomers
Aldohexose : stereoisomers = 24
Ketohexose : stereoisomers = 23
11
1. D-isomer  most found in nature
2. L-isomer
Aldohexose : 24 = 16= D-isomer (8), L-isomer (8)

12. D-isomer and L-isomer are mirror images of each other
(stereoisomers) and cannot be superimposed on each other. Such
molecules with these properties are called enantiomers.
Enantiomers

13. = Two sugars differ only in the configuration around one carbon atom
D-glucose and D-mannose ( C2)
D-glucose and D-galactose ( C4)
D-erythrose and D-threose ( C2) 13
Epimer

14. (Fischer
projection)
D-Aldose
14

15. D-Ketose
15

16. O
O
Common monosaccharides have cyclic structures
16
Intramolecular
hemiacetals /
hemiketals

17. Formation of two
Cyclic forms of
D-glucose
Occurs an addition
asymmetric C atom
produces 2 stereoisomers, designated
 and  -anomer
mutarotation
-D-glucopyranose
-D-glucopyranose
17
D-glucose

18. C
OH
CH2OH
H
HOH2C
OH H
H
C
C
C
HO
O
C
CH2OH
OH
H
HOH2C
OH H
H
C
C
C
HO
O
4
2
3
5
1
6
1
2
3
4
5
6
- D-fructofuranose -D-fructofuranose
OH group at anomeric carbon is on the opposite side of the sugar ring from the CH2OH group : D-isomer
OH group at anomeric carbon is on the same side of the sugar ring from the CH2OH group : L-isomer
18
D or L-isomer from ring structures

19. Chair form Boat form
the chair form is more
stable because it is less
sterically hindered by
neighboring substituents.
19
3-Dimentional conformation

20. Derivatives of the monosaccharides
1. Oxidation reactions :
20
1.1 mild oxidation : the conversion of aldehyde group to a carboxylic acid.
“Aldonic acids”
: Food additive (acidity regulators)
Aldonic acid name: appending the suffix “-onic acid” to the root name of the
parent aldose.
Reducing sugar

21. 1.2. specific oxidation: the conversion of CH2OH group to a
carboxylic acid. “Uronic acids”
Uronic acid name: appending the suffix “-uronic acid” to the root
name of the parent aldose
Importance components of many polysaccharides 21

22. Both aldonic and uronic acids have a strong tendency to internally
esterify, called as lactone.
22
Free aldonic acids are
in equilibrium with
lactones

23. 2. Reduction reactions
23
Derivatives of the monosaccharides
- made by reducing the carbonyl group of a sugar.
- The resulting polyhydroxy compounds are called alditols.
alditols name: appending the suffix “-itol”
to the root name of the parent aldose

24. 3. Deoxy sugars : an OH group is
replaced by atom H
24
Derivatives of the monosaccharides
4. Phosphate sugars: made by
esterifying a phosphate group to one of
the hydroxyls.
5. Amino sugars : made by replacing
a hydroxyl of a sugar with an amine
group (NH2) or delivative NH2
(acetylated amino, NHCOCH3)

25. Oligosaccharides
 Two or more monosaccharides joined covalently by an
O-glycosidic bond.
 O-glycosidic bond : a OH group of one sugar reacts with
the anomeric carbon of the other (= formation of an
acetal from a hemiacetal and an alcohol).
 the resulting compound called a glycoside
 Glycosidic bond are readily hydrolyzed by acid but resist
cleavage by base.
25

26. Formation
of Maltose
26

27. 1. The sequence starts with the nonreducing end at the left using
the abbreviations of Table
The naming rules for Oligosaccharides
27
Based on as follows:

28. 2. Anomeric and enantiomeric forms are designated by prefixes
(e.g., , D-)
3. The ring configuration is designated by the suffixes p (pyranose)
or f (furanose)
4. Numbers in parentheses between residue numbers are used to
identify glycosidic bonds; e.g., (1->4) means a bond from
carbon 1 of the residue on the left to carbon 4 of the residue
on the right.
28
The naming rules for Oligosaccharides

29. 29
The structure of several disaccharides
Lactose: -D-galactopyranosyl-(14)-D-glucopyranose
Sucrose: -D-glucopyranosyl-(1 2)--D-fructofuranoside

30. 30
The structure of
some
oligosaccharides

31. 1. Homopolysaccharides :
single monosaccharides
2. Heteropolysaccharides:
two or more different kinds
of monosaccharides
• also called Glycans
31
Polysaccharides

32. Starch
Contains 2 types of glucose polymers
1. linear polymer ( -Amylose) and 2. branch polymer (amylopectin)
 -Amylose: D-glucose residues connected by  (1 4) linkages
3D: random coil 32

33. Amylopectin
D-glucose residues connected by
 (1 4) linkages, the branch
points, occurring every 24 to 30
residues are  (1  6) linkages.
schematic of starch in an organized structure
33

34. • Like amylopectin, but more extensively branched (every 8-12
residues)
www.emc.maricopa.edu/.../BIOBK/1glycogen.gif 34
Glycogen
• Major form of storage polysaccharides in
animal cells.

35.  Dextrins are a group of low-molecular weight carbohydrates
produced by the hydrolysis of starch or glycogen.
 Dextrins are mixtures of polymers of D-glucose units linked by α-
(1→4) or α-(1→6) glycosidic bonds.
 It is used as adhesive in the manufacture of gummed tapes,
textiles and paper.
35
Dextrin

36.  Dextrans are bacterial and yeast polysaccharides made
up of ( 1  6)-linked poly-D-glucose; all have ( 1  3)
branches, and some also have ( I  2) or ( I  4)
branches
 Dental plaque
Synthetic dextrans =Sephadex = Gel filtration 36
Dextran

37. Cellulose
- Is found in the cell walls of plants
- linear polymer of glucose residues linked by  (1  4)
cellobiose
- Hydrogen bond between the sheets strengthen the structure.
3D:
planar structure
37

38. Chitin
 the principal component in the exoskeletons of crustaceans,
insects, and spiders
 Is present in the cell wall of fungi and algae
 Linear homopolymer of  (1--> 4) linked N-acetyl-D-glucosamine
residues
acetylated amino group 38
Chitosan : a linear polysaccharide composed
of randomly distributed β-(1-4)-linked D-
glucosamine (deacetylated unit) and N-
acetyl-D-glucosamine (acetylated unit).

39. - A family of linear polymers composed of repeating
disaccharide units (uronic acid and hexosamine).
39
Glycosaminoglycans
- involved in a variety of extracellular functions
Hyaluronic acid (“hyalos” Greek = glass) Extracellular matrix

40. 40
The disaccharide repeating units of the common glycosaminoglycan
- Up to 50,000 repeats of the disaccharide unit
- Serve as lubricants in the synovial fluid of joints, the
vitreous humor of vertebrate eye
- extracellular matrix of cartilage and tendons, contributes
tensile strength and elasticity
- Hyaluronidase (pathogenic bacteria, sperm)

41. Heparin is a fractionated form of
heparan sulfate derived mostly from
mast cells (a type of leukocyte).
41
- contributes tensile strength of cartilage,
tendons, ligaments and the wall of aorta.
The disaccharide repeating units of the common glycosaminoglycan

42. 42

- no uronic acid and their sulfate content
is variable
-- present in cornea, cartilage, bone, and
a variety of horny structures formed of
dead cells (horn, hair, nails, ect)
- contributes the pliability of skin.
- present in blood vessels and heart
valves.
-- L-iduronate : 5-epimer of D-glucuronate
(chondroitin sulfate)
The disaccharide repeating units of the common glycosaminoglycan

43. Glycoconjugates
Role
information carriers :
transport proteins, receptors,
hormones, structural protein
• Carbohydrate is covalently joined to a protein or a lipid
such as proteoglycan, glycoprotein, glycolipid
43

44. Oligosaccharide linkages in glycoprotein
44
O-linked : anomeric carbon
linked with OH group of
Serine or Threonine
N-linked : anomeric carbon
linked with NH2 group of
Asparagine

45. 45
Proteoglycans
• glycosaminoglycan-containg
macromolecules of the cell
surface and extracellular matrix
• acts as tissue organizers
• influence various cellular
activities such as growth factor
activation and adhesion
Interactions between cells and the extracellular matrix

46. Proteoglycan
• The basic proteoglycan unit consists of a "core protein" with
covalently attached glycosaminoglycan(s).
• The point of attachment is a Ser residue, to which the
glycosaminoglycan is joined through a tetrasaccharide bridge.
46

47. Proteoglycan aggregates (Supramolecular complex)
47

48. a signal transduction
mediated by cell
membrane-type
proteoglycan
48
Two major groups of
membrane heparan
sulfate proteoglycan :
1. Syndecan :
transmembrane
domain
2. Glypican : lipid
anchor (glycosyl
phosphatidylinositol
(GPI)
Transmembrane proteoglycan

49. 49
peptidoglycan
• peptide-polysaccharide complex
Bacteria classification : Gram positive : thick peptidoglycan
(Gram strain) Gram negative : thin peptidoglycan
linear copolymer of N-acetylglucosamine (GlcNAc) and
N-acetylmuramic acid (Mur2Ac) linked by (14) glycocidic bonds
and cross linked by short peptides attached to the Mur2Ac.

50. Gram positive Staphylococcus aureus
50

51. Gram negative
E.coli
51

52. Glycolipid
• Oligosaccharide head group of
glycolipid of Blood group
• Gangliosides 52

53. Questions
53