BIO211: 211 FUNDAMENTALS OF

BIOCHEMISTRY
• Course outline
• Structural and biochemical organization of cell.
• Prokaryotic and Eukaryotic cells.
• Cell organelles and functions.
• Structure, composition and function of
biomembranes: transport across the membrane.
• Biochemistry of carbohydrates,
• Biochemistry of proteins
• Biochemistry of Lipids
• Biochemistry of Nucleic acids
 CELL
• The term cell is as a mass of protoplasm
limited in space by a plasma membrane and
possessing a nucleus and other organells.
• The establishment of the fundamental
concepts and theories of cell has led to rapid
progress of knowledge in cell biology.
• Modern cell biology has three aspects:
• Cytology, the study of cellular structure and
diversity and is tied up with development of
microscopy
• Cytochemistry, study of chemical constituent
and function of a cell;
• Cytogenetics, the study of the role of cell
structures in inheritance and reproduction
 THE CELL THEORY
• The cell theory is based on the concept that
cell is the basic unit of life. It has four
concepts:
• All living things consist of basic unit called cell;
• Every cell is derived from a preexisting cell
(Schwann and Schleiden);
• A cell is the reproductive unit of cellular
organisms (Rudolf Virchow, 1858)
• The chemical reactions of an organism that is its
metabolism, both anabolism and catabolism
takes place in the cells
• EXCEPTIONS OF CELL THEORY
• Like other generalizations, cell theory has
exceptions.
• 1. PROTOZOA: If applied to the protozoa such as
Paramecium, it is a single cell but has mouth,
contractile vacuole for elimination of waste,
other vacuoles for digestion, and cilia for motility.
 2. VIRUSES
• Without a host cell, viruses cannot carry out
their life-sustaining functions or reproduce.
• They cannot synthesize proteins, because they
lack ribosomes and must use the ribosomes of
their host cells to translate viral messenger
RNA into viral proteins.
 GENERAL CELL STRUCTURE

• Classification of Cells: Cells are classified

based on cellular organization .The two classes
include: Prokaryotic cells e.g. E.Coli and
Eukaryotic cells
• PROKARYOTIC CELLS :-( PRIMITIVE CELLS)
• Prokaryotes do not have a true nucleus and
lack membrane bound organells, yet they
exhibit all characteristics of life. They include
bacteria and cyanobacteria (blue-green algae).
•
 CHARACTERISTICS OF PROKARYOTIC CELLS

• Has a minimum of internal organization and

smaller in size
• Does not have any membrane bound
organelles.
• DNA is not complex with histones. Histones
are not found in prokaryotic cells
• They reproduce asexually through Binary
fusion
CHARACTERISTICS OF
PROKARYOTIC CELLCONTINUATION
• Prokaryotes lack an organized nucleus and
other membrane-bound organelles.
• Prokaryotic DNA is found in a central part of
the cell called the nucleoid.
• The cell wall of a prokaryote acts as an extra
layer of protection, helps maintain cell shape,
and prevents dehydration.
• Prokaryotic cell size ranges from 0.1 to 5.0 μm
in diameter.
 EUKARYOTIC CELLS:
• Are more complex cells with nucleus and many
organelles. They include such organisms as protozoa,
fungi, algae (green, brown and red), and all plant and
animal cells
CHARACTERISTICS OF EUKARYOTIC CELLS:
• Has considerable degree of internal structure
organization with a large number of distinctive
membrane bound organells, having specific
functions.
• Nucleus is the site for genetic informational
components collectively called chromatin
• Sexual reproduction involves both mitosis and
meiosis
• The respiratory site is the mitochondria
• In plant cells, the site of the conversion of
radiant energy to chemical energy is the highly
structural chloroplasts
Typical animal cell
Typical plant cell
The Cytoplasmic Organelles

Nucleus, ribosomes lysosomes, Golgi

bodies and peroxisomes,
mitochondrion
 The Nucleus

Structure of the Nucleus

• The cell nucleus is an oval or spherical and the largest
organelle, surrounded by concentric pair of membranes called
nuclear envelope.
• The outer membrane is continuous with endoplasmic
reticulum and has ribosomes on it.
• The nucleus and cytoplasm are connected through numerous
nuclear pores, which are plugged with circular structures
called annuli (sing: annulus).
• Both the annuli and the pore together form nuclear pore
complex.
• The annulus contains ground granules involved in opening and
closing of the pore.
• The nuclear pore selectively control and regulate passage of
biomolecules between nucleus and cytoplasm.
• The inner nuclear membrane surrounds a fibrous protein
meshwork called nuclear lamina, which organize the nuclear
pore complex and chromosomes, and also shapes the
nucleus.
• The nuclear matrix called karyoplasm or nucleoplasm, contain
chromosome (DNA), RNA and proteins.
 ii) The Nucleolus

• Nucleolus, also called Plasmosome, is present in all

eukaryotic nuclei except sperm,
• It is centrally placed in the nucleus and has two parts
namely:
• Pars amorphosa, a region filled with microfilaments
• Nucleolema, a network of chromatin material,
which contain the DNA molecules.
• Nucleolus is the site for synthesis of ribosomes
 Functions of the Nucleus
• It is the site for synthesis of nucleic acids:
DNA, mRNA, tRNA, and 5S-RNA.
• It is responsible for storage, preservation,
replication, and expression of genetic
information.
 Lysosomes

• Are membrane-bound organelles believed to

originate from the Golgi body
• They are specialized for intracellular digestion
and are rich in hydrolytic enzymes called acid
hydrolases.
• The shape, size and internal structure of
lysosomes vary from cell to cell depending on
their physiological activities.
 Hydrolytic functions of lysosomes
• NOTE: The hydrolytic functions of lysosomes can
be divided into four categories:
• i) Autophagy: Old organelles or macromolecules
trapped in autophagic vesicles fuses with
lysosomes and are digested by lysosomal
enzymes.
• ii) Heterophagy: Foreign materials contained in
pinosomes or phagosomes fuses with lysosomes
and are digested by lysosomal enzymes.
• iii) Autolysis: This occurs when there is
malfunction or disease in a cell causing the
lysosomes to rapture and release their enzymes,
which then digest and kill the whole cell.
• iv)Crinophagy: In this process, waste and
undigested materials accumulated in excretory
vesicles, fuse with lysosomes and are degraded.
• The waste from lysosomal action is accumulated
into vesicles called residual bodies, which are
expelled from the cell by exocytosis
 The Ribosomes
• Ribosomes are engines used by the cell for
protein synthesis, and are uniform in size,
structure and composition in different cells.
• The number and concentration of ribosomes is
directly related to RNA content of the cell and the
basophilic properties of the cytoplasm.
• Ribosomes are submicroscopic particles
composed of rRNA and proteins in almost equal
proportions.
• There are two main sizes of ribosomes namely
70S (prokaryotic) and 80S (eukaryotic), based
on sedimentation coefficients by
ultracentrifugation
• In both cases the ribosomes appear as an
oblate spheroid structure with a cleft that
divides it into larger and smaller subunits.
• The subunits require low concentration of
Mg2+ for structural cohesion
 The Golgi apparatus

• Golgi complex, also called golgi body or golgi

apparatus, consists of a series of flattened
membranous cavities (cisternae) stacked
together.
• In plants cells, it is called dictyosome.
• It is rich in glycosyl transferase enzyme besides
thiamine pyrophosphatase, acid phosphatase and
other hydrolases of lysosomal type.
• When proteins from ER lumen are transferred
into golgi lumen, they are covalently modified in
various ways to produce their final mature form.
 Functions of golgi apparatus
• It is concerned with separation and packaging of
materials processed in ER for export.
• Synthesis of carbohydrate-rich compounds. Both
ER and golgi complex are functionally integrated
to provide sites for synthesis and modification of
proteins, glycoproteins, glycolipids, lipoproteins,
phospholipids and steroids, and polysaccharides.
• Plays important role in cell wall formation by
accumulating cellwall polysaccharides.
 Peroxisomes
• Peroxisomes are single membrane-enclosed
organelles and contain proteins called
peroxins.
• Peroxisomes replicate by division and can also
be regenerated even if entirely lost from the
cell.
• Most human cells contain about 500
peroxisomes.
 Role of peroxisomes in animals
• In animal cells, fatty acids are oxidized in both
peroxisomes and mitochondria, but in yeast and plants,
fatty acid oxidation is restricted to peroxisomes.
• In animal cells, peroxisomes are also involved in
biosynthesis of lipids, cholesterol, dolichol and amino
acid, lysine,
• In the liver, peroxisomes are involved in synthesis of
bile acids, which are derived from cholesterol.
• In addition, peroxisomes contain enzymes for the
synthesis of plasmalogen (a phospholipid), a
component of heart and brain tissue
 Roles of peroxisomes in plants
• Peroxisomes in seeds (then called glyoxysomes)
are responsible for conversion of fatty acids into
carbohydrates through the glyoxylate pathway.
• Peroxisomes in leaves are involved in
photorespiration, which metabolize glycolate
(side product of photosynthesis) to glycine.
• Glycolate is formed when Calvin cycle utilizes O2
instead of CO2, which appears to be an inherent
property of rubisco (ribulose bisphosphate
carboxylase) of the calvin cycle.
 Mitochondrion

• Mitochondrion is an ovoid double membrane

structure whose inner membrane is convoluted to
form cristae.
• It is present in all eukaryotic cells except
mammalian erythrocytes.
 MORPHOLOGY-SHAPE

• The shape of mitochondrial varies according

to the type of cell.
• In general they are sausage shape or
filamentous.
• Depending upon the physiological conditions
they may be club-shaped, tennis recket-
shaped, rod shaped or vescular in shape.
• Such shapes are only for a short period and
after 48 hours these changes cease and the
mitochondria regain their original form.
ULTRASTRUCTURE
 Ultrastructure
• Ultrastructure reveals that they consist of two membranes
(inner and outer) and two compartments.
• The larger compartment contains the mitochondrial matrix.
• Each mitochondrion is surrounded by an outer limiting
membrane .
• Inner membrane projects into mitochondrial cavity certain
complex in folding called mitochondrial crests or cristae.
• The space between outer and inner membrane is called
innermembrane space.
• The inner membrane divides the mitochondrion into two
chambers
FUNCTIONS OF MITOCHONDRION

• Mitochondrion synthesizes respiratory

enzymes
• It actively imports some proteins from ER by
receptor-mediated mechanisms which exploit
ATP and electrochemical gradient
• Mitochondrion is the principle site of ATP
synthesis but is also involved in other
metabolic functions discretely assigned to
various compartments
 Structure of Biomembranes:

• Biomembranes structure has been proposed

and explained by Fluid Mosaic model.
 THE FLUID MOSAIC MODEL

• Most convincing model. According to this membrane lipids are

in form a fluid bilayers and the membrane is three-
dimensional
• The lipid molecules are closely packed and arranged such that
the hydrophobic tails lie within the bilayers.
• Peripheral proteins: are superficially located on the bilayers
whereas integral proteins penetrate into the interior of the
membrane.
• The sum of hydrophobic and hydrophilic interactions of
proteins and phospholipids provide the fluidity of the
membrane.
• Membranes of many internal organelles have similar structure
because they are formed from infoldings of plasma
MEMBRANE TRANSPORT

Transport: An essential role of biomembranes that

allows movement of all compounds necessary for the
normal function of cell across the membrane barrier.
These compounds include: Sugars.amino acids, fatty
acids,steroids,cations and anions, water
 TYPES OF TRANSPORT MECHANISMS

• Mechanisms involved in transport of substances a cross a

membrane fall into two categories
• Passive and Active
• PASSIVE TRANSPORT CATEGORY: Include physical
mechanisms in which the forces that drive substances a
cross membrane are supplied from the environment of the
cell and these are Diffusion and Osmosis.
• They are devided into two: simple diffusion and facilitated
diffusion.
• ACTIVE TRANSPORT CATEGORY: Include complex reactions
which utilize the free energy ( ATP produced by cells own
metabolism and they move substances against
concentration or electrochemical gradient.
Simple diffusion
• In simple diffusion the
substance passes through
a membrane without the
aid of an intermediary
such as an integral
membrane protein.
• The types of molecules
that can do this are
themselves substantially
hydrophobic in nature as
carbondioxide, oxygen
and ethanol.
 FACILIATED DIFFUSION

• It is similar to simple diffusion i.e. solutes

move along the concentration gradient this
enable the transport of neutral molecules)
• NOTE: Neutral molecules do not easily pass
through the non-polar region of the
membrane, a special enzyme called permease
help to transfer them into the interior of the
cell
• For charged groups (ion) and too large neutral
molecules, their passage is facilitated by
specific carrier proteins, which binds to the
molecule and ferries it across the membrane.
 MECHANISM OF FACILITATED
TRANSPORT
• Mechanism of facilitated diffusion has been
explained by PING-PONG MODEL
• It states that this type of diffusion is facilitated
by carrier proteins.
• Carrier protein exists in two principal
conformations depending on the solute
concentration i.e. Pong and Ping STATES.
• PONG STATE: In the pong state carrier protein is
exposed to high concentrations of solutes and
molecules of solutes bind to specific sites on the carrier
protein. This occurs in lipid bilayers of the cell with high
solute concentration.
• PING STATE: In inner side, conformational change
occurs to ping state and the solute is dissolved to the
side favoring new equilibrium.
• The empty carrier protein then reverts to the original
conformation pong state to complete the cycle.
• Example.D-fructose is absorbed from intestine by
facilitated diffusion.
FACTORS DETERMINING FACILITATED
TRANSPORT
• Concentration gradient across the membrane.
• The amount of carrier protein a available ( Key
control system)
• Rapidity of solute-carrier concentration
• Rapidity of conversion of conformation state
pong to ping and vice versa
 ACTIVE TRANSPORT

• System of transport that occurs against

concentration gradient and Electrical gradient
hence needs energy.
• The system also requires the mediation of
specific carrier or transport proteins.
• The major sources of energy for active
transport are ATP hydrolysis and electron flow
linkages occurring in respiratory and
photosynthetic pathways.
 MOLECULES TRANSPORTED VIA ACTIVE TRANSPORT

• Inorganic
• Amino acids
• Carbohydrates
Important features of active transport system are
• They depend on metabolic processes yielding ATP
• They are solute-specific transport mechanisms
• They are direction-specific, e.g. most cells pump K+ inwards and Na+
outwards only.
• Their activity depends on concentration of substances being transported.
• They can be selectively inhibited; e.g. Ouabain inhibits Na+ transport.
• As a result of integrated action of active transport mechanisms, internal
solute and ion composition of cells is maintained at constant levels despite
fluctuations in the surrounding.
 TRANSPORT OF BULK AND
MACROMOLECULES
• The mechanism of transport of
macromolecules such as Proteins, hormones,
immunoglobulin, low density lipoproteins and
even Viruses takes place across the membrane
by two independent mechanisms
• Endocytosis and Exocytosis
• ENDOCYTOSIS: Aprocess by which nutrient or other
materials are ingested (engulfed) in bulk by a cell)
• Endocytosis vesicles are formed when segments of
plasma membrane invaginates enclosing a minute
volume of extracellular fluid ( ECF) its contents.
• The vesicle then pinches off as the fusion of plasma
membranes seal the neck of the vesicle at the original
site of invagination.
• The vesicle fuses with other membrane structures and
thus transport of its contents to other cellular
compartments.
 FACTORS REQUIRED FOR ENDOCYTOSIS

• Energy usually derived from ATP hydrolysis

• Calcium ions
• Contractile element in the cell-probably the
micro-filament system.
 FATE OF VESICLES

• Most endocytic vesicles fuse with primary

lysosomes to form secondary lysosomes which
contain hydrolytic enzymes and are
specialized organelles for intracellular
disposal.
• Vesicular contents are digested liberating
simple sugars, amino acids e.t.c which diffuse
out of the vesicles to be reutilized in the
cytoplasm.
 BIOCHEMISTRY
 A science concerned with the chemical basis of life
 It can also be described as the science concerned with
the chemical constituents of living cells and with the
reactions and processes they undergo.
 All chemical constituents of living things are contained
in the cell.
CONT’D
 By this definition, biochemistry encompasses large
areas of cell biology, molecular biology and
molecular genetics
Note:
 All biochemical reactions take place in a cell, which is
defined as the structural unit of living systems
 All living things are made up of mass of cells
OBJECTIVE
 The major objective is to understand molecular level,
of all of the chemical processes associated with living
cells.
 To achieve this objective, biochemists have sought to
isolate the numerous molecules found in cells,
determine their structures, and analyze how they
function using various biochemical techniques such
electrophoresis e.t.c
 CELL
 Defined as a mass of protoplasm limited in space by a
plasma membrane and possessing a nucleus.
 Modern cell biology has three aspects:
i) Cytology: the study of cellular structure and diversity
and is tied up with development of microscopy;
ii) Cytochemistry: study of chemical constituent and
function (biochemistry) of a cell;
iii)Cytogenetics:the study of the role of cell structures
in inheritance and reproduction.

 Cells Contain a Universal Set of
Small Molecules
 All cells contain a collection of 100 to 200 different
small organic molecules.
 This collection of molecules includes the common
amino acids, nucleotides, sugars and their
phosphorylated derivatives, and a number of mono-
,di-, and tricarboxylic acids.
 The molecules are polar or charged, water soluble, and
present in micromolar to millimolar concentrations.
 They are trapped within the cell because the plasma
membrane is impermeable to them
 Note: Cells have specific membrane transporters that
catalyze the movement of some molecules into and
out of the cell or between compartments in eukaryotic
cells.
Macromolecules Are the Major
Constituents of Cells
 Many biological molecules are macromolecules,
polymers of high molecular weight assembled from
relatively simple precursors and include ;
 Proteins, nucleic acids, and polysaccharides which are
produced by the polymerization of relatively small
compounds with molecular weights of 500 or less.
Molecular Components of an E. coli
Cell
GENERAL CELL STRUCTURE

Classification of Cells
 Cells are classified based on cellular organization .The two
classes include:
I)Prokaryotic cells e.g. E.Coli
 Prokaryotes do not have complex systems of membranes
and organelles, yet they exhibit all characteristics of life.
They include bacteria and cyanobacteria (blue-green
algae).

➢ Eukaryotic cells e.g. animal cells, plant cells

CHARACTERISTICS OF PROKARYOTIC CELLS
 Has a minimum of internal organization and smaller
in size
 Does not have any membrane bound organelles.
 DNA is not complex with histones. Histones are not
found in prokaryotic cells
 It is respiratory system is closely associated with its
plasma membrane
 Its sexual reproduction does not involve mitosis or
meiosis .Binary fusion
 EUKARYOTIC CELLS

 Are more complex cells with nucleus and many

organelles.
 They include organisms such as
➢ Protozoa,
➢ Fungi, algae (green, brown and red),
➢ All plant and animal cells
CHARACTERISTICS OF EUKARYOTIC
CELLS
 Has considerable degree of internal structure with a
large number of distinctive membrane, enclosed
having specific functions
 Nucleus is the site for informational components
collectively called chromatin
 Sexual reproduction involves both mitosis and meiosis
 The respiratory site is the mitochondria
 In plant cells, the site of the conversion of radiant
energy to chemical energy is the highly structural
chloroplasts
 Cell Size and Shape
 SHAPE: There is no generalization in shape, size and structure of eukaryotic and
prokaryotic cells.
 The shape of a cell depend on varies factors

✓ functional adaptations and partly on the surface tension and viscosity of the
protoplasm
✓ the mechanical action exerted by the adjoining cells (in case of multicellular
organisms)
✓ the rigidity of the cell membrane or cell wall.

 Note: Some cells are irregular and change their shape frequently, for example,
amoeba and leucocytes
Shapes of Various Cells
 SIZE
 Factors that determine maximum cell size
• Nuclear cytoplasmic relations
• Metabolism
• Intracellular activities
 NOTE: The two main constraints of cell size are
surface area/volume ratio and compartmentalization
 HOME WORK
 Students to read and make notes on
➢ surface area/volume ratio
➢ compartmentalization
 PINOCYTOSIS

• FLUID PHASE PINOCYTOSIS- It is induced by materials

in solution and is non-specific, i.e. there is no selective
recognition of materials to be ingested
• Once the solution is in contact with the plasma
membrane, the membrane invaginates into the cell
interior to form vesicles called pinosomes
• The pinosomes bud off the membrane and empty their
contents into the cytoplasm
• Endocytosis is an active process that requires energy.
It is observed in amoeba and, endothelial cells lining
blood capillaries.
BIOCHEMISTRY OF
CARBOHYDRATES

LECTURER: CAROLINE JK

1
 BIOCHEMISTRY OF
CARBOHYDRATES
• Carbohydrates are biomolecules that contain
the elements carbon, hydrogen and oxygen. The
latter two are in the same ratio as in H2O, hence
the name carbohydrate. Carbohydrates are of the
nature of polyhydroxyaldehydes or ketones.
• They are also called ‘Saccharides’ (i.e.
‘Sakcharon’ in Greek) meaning sugar

2
 Carbohydrate classification
1.Monosaccharides (e.g., glucose, fructose).
2.Disaccharides consist of two monosaccharide
units linked together by a covalent bond (e.g.,
sucrose).
3.Oligosaccharides contain from 3 to 10
monosaccharide units (e.g., raffinose).
4.Polysaccharides contain very long chains of
hundreds or thousands of monosaccharide
units, which may be either in straight or 3
 MONOSACCHARIDES
• Monosaccharides are the simplest form of
sugars and are the most basic units of
biologically important carbohydrates. Biological
important ones have three to six carbon atoms
(i.e. 3-Trioses, 4-tetroses, 5-pentoses, and 6-
hexoses).
• They exist as either aldoses or ketoses

4
 Aldoses and ketoses
• Monosaccharides are classified into 2 i.e those
with aldehyde group (CHO) are called aldoses
and those with ketone (C=O) group are called
ketoses.
For aldoses, the aldehyde group is located at
carbon number 1 while for ketoses the ketone
group are located at number 2.

5
 Cont…
Both ketone and aldehyde groups are the
reactive groups of monosaccharides.
They have several names which include
• Carbonyl carbon, hemiacetal group, hemiketal
groups,anomeric carbon, and reactive carbon

BIO 210 Lecture notes By J. Kemmey 6

 Properties of monosaccharides
1.Monosaccharides are colourless, crystalline
compounds readily soluble in water and have
sweet taste.
2.They are solids at room temperature.
3. Ther are colourless.
4.They are extremely soluble in water:

7
 Properties of monosaccharides
4.Despite their high molecular weights, the
presence of large numbers of OH groups make
the monosaccharides much more water soluble
than most molecules of similar MW. E.g Glucose
can dissolve in manute amounts of water to
make a syrup (1 g / 1 ml H2O).

8
 Properties continuation
5. They are optically active since they rotate the plane
of polarized light either to the left or to the right. Those
that rotate to the left are L- monosaccharide e.g L-
glucose while those that rotate to the right are called D-
monosaccharide e.g D-glucose. L stands for
Levorotatory while D stands for Dextrorotatory

9
 CONT…
Often, living systems contain only one of the possible
stereochemical forms of a compound, or they are found
in separate systems e.g D-lactic acid is found in living
muscles while L-lactic acid is present in sour milk. In
some cases, one form of a molecule is beneficial, and
the enantiomer is a poison (e.g., L- thalidomide).
Humans can metabolize D-monosaccharides but not L-
monosaccharide; only L-amino acids are used in protein
synthesis
10
 CONT..
6.They show structural Stereoisomerism- A
substance is said to exist as sterioisomer when it exist in
two different forms due to different configuration of the
atoms within the same molecule.- e.g glucose can exist
as L and D glucose or α- or ß- glucose

11
6. They are exhibit chirality. A molecule is said to
be chiral when it has a carbon atom is attached
to four different groups.
NB some carbons in monosaccharides are chiral
Chirality is well illustrated in fischer projection

12
 Fischer projection of
monosaccharides
• This is the represention of monosaccharides using horizontal
and vertical lines.
• In the projection, horizontal lines show groups that project
above the plane of paper towards the viewer and the verticle
lines show groups that project below the plane of the paper
from the viewer
• It is used to represent both Aldoses and ketoses
• Fisher projection shows chiral carbons and
sterioisomers (epimers).

13
Fischer projection of monossacharides-aldoses

14
Fischer projection of monossacharides-aldoses
cont

15
Fischer projection of monossacharides-ketoses

BIO 210 Lecture notes By J. Kemmey 16

Fischer projection of monossacharides-ketoses
cont

17
Examples of D and L forms of monosaccharide represented in
fischer projecton

18
 Cont…
• The designation D and L is based on the configuration of OH
at the asymmetrical carbon (or chiral) atom (atom in which four
different atoms or groups are attached) , located furthest from
carbonyl functional group. This carbon is called penultimate
carbon atom.
• Fischer projections provide a convenient way to represent
sterioisomers which are epimers. Any two sugars which differ
from each other only in configuration around a single chiral
carbon other than the carbonyl carbon are called epimers. For
example, D-Glucose and L- glucose, D- glucose and D-
galactose; D-Glucose and D- mannose.
19
 Haworth projection
In solution, most sugar molecules occur in ring form
rather than linear form. Expressing structures of sugars
in ring form is called Haworth projection formula. For
aldose the cyclic structures are called hemiacetals while
for ketoses the cyclic structures are called hemiketals.
The ring structures are either 6- membered ring called
pyranose e.g glucose or a 5-membered ring called
furanose e.g fructose.

20
Six membered ring (pyranose) and
five membered ring (furanose)

21
haworth projection of GLUCOSE

22
 Haworth projection Cont…
• In ring form, sugars exists either as α- or ß- isomeric
forms. In α-isomer, the OH on C-1 phases direction
opposite the O-member of the ring, whereas in ß-
isomer the OH of C-1 phases same direction as O
member. Such isomers that differ in configuration
only around anomeric carbon (C-1 for aldoses or C-2
for ketoses) are called anomers. For example, α-D-
Glucose and ß-D-Glucose. The interconversion
between α-isomer and ß-isomer forms is called
mutarotation

23
Cont…

24
Haworth projection of different
molecules

25
Continuation haworth projection

26
Important Monosaccharides

27
Important Monosaccharides

28
 Oxidation of Monosaccharides
• Aldehydes and ketones that have an OH group on the
carbonly carbon and can reduce CUPROUS IONS TO CUPRIC
IONS WHILE IT SELF OXIDISED TO CARBOXYLIC ACID. Sugars
that undergo this reaction are called reducing sugars. (All of
the monosaccharides are reducing sugars.)

29
 Disaccharides and Oligosaccharides
Disaccharides
• Two monosaccharides can be linked together through a
glycosidic linkage to form a disaccharide.

30
 Cont’d
• Lactose is a major carbohydrate in milk, is a
disaccharide synthesized only in lactating mammary
glands The naturally occurring anomer of lactose is
sweeter and more soluble than the anomer. The
anomer can be found in stale ice cream, where it has
crystallized during storage and given a gritty texture
to the ice cream. Lactose is joined by β-1,4Glycosidic
bond
• Maltose is a disaccharide released during the hydrolysis
of starch, which is a polymer of glucose residues. It is
present in malt, a mixture obtained from corn or grain
that is used in malted milk and in brewing. Maltose is
joined by α-1,4 glycosidic bond
31
Sucrose is the most abundant disaccharide found in
nature, is synthesized only in plants
• Disaccharides that contain a free OH groups at the
anomeric groups are reducing sugars. I.E maltose and
lactose are reducing sugars while sucrose is non
reducing sugar since all the OH groups at the reactive
groups (anomeric groups) have been used to form a
bond. The reactive groups in sucrose are Carbon
number 1 in glucose and carbon number 2 in fructose.
The bond joining sucrose is α-1,2 glycosidic bond

32
 Polysaccharides
• Most carbohydrates found in nature occur as polysaccharides,
polymers of medium to high molecular weight.
• Polysaccharides also called glycans, differ from each other in the
identity of their recurring monosaccharide units, in the length o f
their chains, in the types o f bonds Iinking the units, and in the
degree of branching.
• Homopolysaccharides contain only a single monomeric species;
heteropolysaccharides contain two or more different kinds .
• Some homopolysaccharides Serve a s storage forms of
monosaccharide that are used as fuels; e.g starch and glycogen.
• Other homopolysaccharides, serve as structural elements in plant
e.g cellulose and chitin cell walls and animal exoskeletons.
• Heteropolysaccharides provide extracellular support for organisms
of allkingdoms. E.g, the rigid layer of the bacterial cell envelope( the
peptidoglycan) is composed in part of two alternating
monosaccharide units
33
 Starch
• Starch contains two types of glucose polymer, amylose and
amylopectin.
• Amylose consists of long, unbranched chains of D-glucose
residues connected by (α-1, 4) glycosidic linkages (as in
maltose)
• Such chains vary in molecular weight from a few thousand to
more than a million.
• Amylopectin also has a high molecular weight (up to 200
million) but unlike amylose is highly branched. The glycosidic
linkages joining successive Glucose residues in amylopectin
chains are (α-1, 4 glycosidic linkage); the branch points
(occurring every 24 to 30 residues) are (α-1,6) Iinkages.

34
 Glycogen
• the main storage polysaccharide of animal cells. Like
amylopectin, glycogen is a polymer of (α-1,4)-linked
subunits of glucose with (α-1,6)-Iinked branches, but
glycogen is more extensively branched (on average
every 8 to 12 residues) and more compact than starch.

• abundant in the liver constitute about 70%

35
36
 Structural homopolysaccharides
cellulose
• Cellulose is a, fibrous, tough, water-insoluble substance
• found in the cell walls of plants, particularly in stalks, stems,
trunks, and all the woody portions of the plant body.
• Cellulose constitutes m much of the mass of wood, and cotton
is almost pure cellulose. Like amylose, the cellulose is a linear,
unbranched homopolysaccharide, consisting o f 10,000 to
15,000> glucose units
• The glucose residues in cellulose are linked by β-(1,4)
glycosidic bonds, in contrast to the (α-1,4) bonds of amylose.
This difference gives cellulose and amylose very different
structures and physical properties.

37
 Chitin
• Chitin is a linear homopolysaccharide composed of N-acetylglucosamine
residues in β-(1,4) Iinkage.
• The only difference from cellulose is the replacement of the hydroxyl
group at C-2 with an acetylated amino group.
• Chitin is the principal component of the hard exoskeletons of nearly a
million species of arthropods e.g-insects, Iobsters,and crabs, -

38
 Glycoproteins
• Carbohydrates can be linked to proteins to form glycoproteins
• Carbohydrate groups are covalently attached to many different proteins to
• form glycoproteins
• There are three classes of glycoproteins
• 1. Glycoproteins
• 2. Proteoglycans
• 3. Mucins or Mucoproteins
• Glycoproteins:- the protein component is the largest component by
weight.
• A versatile class playing a variety of biochemical roles
• Many are components of cell membranes involved in processes such as
adhesion and binding of sperms to eggs
• Many proteins secreted from cells are glycosylated or modified by the
attachment of carbohydrates
BIO 210 Lecture notes By J. Kemmey 39
 Proteoglycans
• The protein component is conjugated to a particular type of
polysaccharide called Glycosaminoglycan
• The carbohydrate component constitutes a larger percentage by weight of
the proteoglycan compared with simple glycoproteins
• Proteoglycans function as structural components and lubricants
• 3. Mucin mucopolysaccharides, like proteoglycans are predominantly
carbohydrates
• N- acetyl galactosamine is the carbohydrate moiety bound to proteins
• Carbohydrates are linked to proteins through the asparagine (N-linked) or
through serine or threonine (o-linked residues

40
 Extracellular Matrix Heteropolysaccharides
Glycosaminoglycans
• The extracellular space in the tissues of multicellular animals is filled with
a gel-like material, the extracellular matrix (ECM), also called ground
substance, which holds the cells together and provides a porous pathway
for the diffusion of nutrients and oxygen to individual cells.
• ECM is composed of an interlocking meshwork of heteropolysaccharides
called glycosaminoglycans,
• are a family of linear polymers composed of repeating disaccharide units .
They are unique to animals and bacteria and are not found in plants.
• One of the two monosaccharide is always either N-acetylglucosamine or
N-acetylgalactosamine; the other is in most cases a uronic acid, usually D-
glucuronic or L-iduronic acid
• Some glycosaminoglycans contain esterified sulfate groups. The
combination of sulfate groups and the carboxylate groups of the uronic
acid residues gives glycosaminoglycans a very high density of
• negative charge
41
 hyaluronan (hyaluronic acid)
• hyaluronan (hyaluronic acid) contains alternating residues of D-glucuronic
acid and N-acetylglucosamine made up to 50, 000 repeats of the basic
disaccharide unit;
• it forms clear, highly viscous solutions that serve as lubricants in the
• synovial fluid of joints and give the vitreous humor of the vertebrate eye
its jellylike consistency (the Greek hyalos means "glass"; hyaluronan can
have a glassy or translucent appearance).
• Hyaluronan is also a component of the extracellular matrix of cartilage and
tendons, to which it contributes tensile strength and elasticity as a result
of its strong interactions with other components of the matrix.

BIO 210 Lecture notes By J. Kemmey 42

43
 Amino Acids
• An amino acid consists of an amino group, a carboxyl group, a
hydrogen atom and a distinctive R group. The carbon to which
the amino group and R group are attached is called α-carbon.
The R group determines the individuality of an amino acid and
is referred as the side chain. There are twenty amino acids that
make proteins classified as essential and nonessential
• The amino acids are classified by:
• 1. the polarity of the R group side chains, and
• 2. the presence of either acidic or basic group
• Subdivided into four groups
– neutral, nonpolar
– neutral, polar
– basic, polar (contains an additional amino
group)
– acidic, polar (contains an additional
carboxylate group)
• All of the amino acids are also known by a
three-letter and one-letter abbreviations
The Common Amino Acids
 Stereochemistry of the Amino Acids
• Since the amino acids (except for glycine) contain
four different groups connected to the a-carbon,
they are chiral, and exist in two enantiomeric
forms:
• The amino acids in living systems exist primarily
in the L form.
 Essential and non Essential amino acids

• Amino acids are classified into essential

and non essential. There are 10 essential
and 10 non essential.
• Essential-The body cannot make hence
must be supplied in diet
• Nonessential- The body can make hence
need not be supplied in diet.
Essential and non Essential amino acids
 Properties of amino acids
• Amino acids are colourless, crystalline
substances generally soluble in polar solvents
such as water, slightly soluble in alcohol but
insoluble in non-polar solvents such as ether
and benzene, with exceptions.
• They have high melting points, usually above
200 C.
o
 Acid base properties of amino
acids
They have both positive and negative charges
hence behaving as an acid or a base when placed
in solutions of varying PH. At acidic PH the
amino acid is protonated hence behaving as a
base while at basic PH the amino acid carries a
negative charge hence behaving as an acid.
Acid base properties of amino
acids
 Acid base properties of amino
acids cont…
At pI, amino acids in neutral solutions
• occur as dipolar ions and are termed
Zwitterions. A molecule with both
• positive and negative charges is called a
zwitterion.
 Peptide Formation
• Amides are formed from the reaction of an
amine and a carboxylic acid:

• In the same way, two amino acids can combine

to form a dipeptide, held together by a peptide
bond:
•
A third amino acid can join the chain to form a tripeptide:
Short chains are referred to as peptides, chains of up to
about 50 amino acids are polypeptides, and chains of
more than 50 amino acids are proteins.
NB amino acids within the polypeptide chain are called
amino acid residues and have their name replaced with
YL where there was INE. E.g alanine becomes yl while
the last amino acid in the polypeptide retains its name.
• Amino acids in the polypeptide chain are named
/numbered from N terminal to C termial
• The N-terminal is the end with NH group while the
C terminal is the end with the carboxylic group.
• The residue with a free amino group is called the
N-terminal residue, and is written on the left end of
the chain.
• –The residue with a free carboxylategroup is called
the C-terminal residue, and is written on the right
end of the chain.
 Functions of amino acids
i) Amino acids are the monomeric constituent s
of proteins and peptides.
ii) Some amino acids are converted to
carbohydrates. They are called glucogenic amino
acids
iii) Specific amino acids give rise to specialized
products. For example, Tyr forms thyroid
hormones, epinephrine and norepinephrine; Gly
are used for synthesis of heme.
 Levels of protein structures
1. Primary structure
• This is the linear sequence of amino acids in a
polypeptide chain.
• It determines the further levels of organization
of protein molecule.
• In primary structure, the amino acids are
numbered from N-terminal (which is always
written on the left end) of the polypeptide
chain.
 2. Secondary structure
• It is formed when a polypeptide chain assumes a
three-dimensional structure by folding or coiling, due
to steric interrelationships between amino acids
located near each other in the chain.
• The tendency of the polypeptide chain is to arrange
itself in space so as to form a tightly compact
structure. Three types of secondary structure are
possible: α-
• helical, reverse turn, and ß-pleated sheet.
 3. Tertiary structure
• It is formed when a polypeptide chain undergo extensive
coiling to produce complex rigid structure and results from
steric interaction between amino acids located far apart but
brought closer by folding, looping and binding.
• The final shape is determined by the intermolecular forces
such as hydrogen bonds, hydrophilic and hydrophobic
interactions, disulfide forces, ionic / electrostatic forces and
van der waals forces.
• The conformations are biologically active and are referred to
as native proteins.
 4. Quatenary structure
It contain more than one polypeptide chain. Each
chain in the molecule has its own characteristic
tertiary structure and is called subunit or
monomer.
The compound structure is called oligomer. For
example, hemoglobin is a tetramer.
 Classes of proteins
• i) Simple Proteins - These are proteins which contain
amino acids only, e.g. globulins, and albumins.
• ii) Conjugated Proteins - These are proteins which
contain other chemical components apart from amino
acids. The non-amino acid part is called prosthetic
group. Examples include nucleoproteins,
glycoproteins, phosphoproteins, lipoproteins and
metalloproteins.
• iii) Derived Proteins - These are produced as a result
of either denaturation or partial digestion of proteins.
 Protein Function
Proteins perform crucial roles in all biological processes.
• 1.Catalytic function: Nearly all reactions in living
organisms are catalyzed by proteins functioning as
enzymes. Without these catalysts, biological reactions
would proceed much more slowly.
• 2.Structural function: In animals structural materials
other than inorganic components of the skeleton are
proteins, such as collagen (mechanical strength of skin
and bone) and keratin (hair, skin, fingernails).
• 3.Storage function: Some proteins provide a way to
store small molecules or ions, e.g., ovalbumin(used by
embryos developing in bird eggs), casein (a milk protein)
and gliadin(wheat seeds), and ferritin(a liver protein
which complexes with iron ions).
• 4.Protective function: Antibodies are proteins that
protect the body from disease by combining with and
destroying viruses, bacteria, and other foreign
substances. Another protective function is blood clotting,
carried out by thrombin and fibrinogen.
 Function cont.
• 5.Regulatory function: Body processes regulated by
proteins include growth (growth hormone) and thyroid
functions (thyrotropin).
• 6.Nerve impulse transmission: Some proteins act as
receptors for small molecules that transmit impulses
across the synapses that separate nerve cells.
(Rhodopsinin vision, xxxxx
• 7.Movement function: The proteins actinand myosin
are important in muscle activity, regulating the
contraction of muscle fibers.32
• Protein Function
• 8.Transport function: Some proteins bind small
molecules or ions and transport them through the body.
• –Serum albumin is a blood protein that carries fatty acids between
fat (adipose) tissue and other organs.
• –Hemoglobin carries oxygen from the longs to other body tissues.
• –Transferrinis a carries of iron in blood plasma.
• •A typical human cell tontains9000 different proteins; the human
 Nucleic acid-Introduction
• Nucleic acids are the molecules that code the
genetic information of organisms. They are DNA
and RNA. They are acid compounds found in nuclei
therefore named nucleic acid. The repeating unit of
nucleic acids is called nucleotide. A nucleotide is
made of a pentose sugar, nitrogenous base and
phosphoric acid. The pentose sugars are D-ribose
and D-2-deoxyribose.
Ribose and deoxyribose
 Nitrogenous bases
• The nitrogenous bases are grouped into two:
i) Purines – Adenine (A) and Guanine (G)
ii) Pyrimidines – Cytosine (C), Thymine (T), and
Uracyl (U)
Purine and pyrimidines and how they
are numbered
 Continuation--
• A nitrogenous base is joined to a pentose sugar
by ß-N-glycosidic bond while the phosphoric
acid is joined to the sugar by O- glycosidic bond.
The phosphate groups are bjoined to each other
via an acid anhydride bond. When a nitrogenous
base is joined to sugar without phosphate group
is called nucleoside.
•
 Cont..
• Nucleotides are joined to one another by
Phosphodiester bonds to form a polynucleotide
which are RNA or DNA. The phosphate groups
in nucleotides are joined by acid anhydride
bonds.
• The name of the base changes the moment its
joined to a sugar
 Table showing name change of bases
when joined to a sugar
base sugar Nucleoside (base:sugar) Nucleotide(base:sugar
and phosphate)
Adenine (A) Ribose Adenosine ATP(Adenosine
trphosphate
Guanine (G) deoxyribose Guanosine dGMPdeoxy Guanosine
Monophosphate
Cytosine (C) deoxyribose Cytidine dCMP(deoxy Cytidine
Monophosphate)
Uracil (U) Ribose Uridine UDP(Uridine
Diphosphate)
Thymine (T) deoxyribose Thymidine DeoxyThymidine
Triphosphate (dTTP)
Joining of the sugar to the base can
form Syn or anti conformation-anti
conformation is common in nature
 DNA STRUCTURE

• DNA structure is classified as primary or

secondary. Primary structure is made of
nucleotides joined to form a single
polynucleotide strand that run from 3’ to 5’.
PRIMARY STRUCTURE
 Secondary structure of DNA
• In secondary structure, DNA molecule consists
of two helical strands which are coiled around a
• common axis to form a right-handed double
helix. The phosphate and deoxyribose units are
found on the periphery whereas the bases occur at
the centre. The two chains are held together by
hydrogen bonds between pairs of bases: A pairs
with T by 2 bonds while C pairs with G by 3
bonds.
HOW BASES PAIR IN secondary structure of DNA
 Secondary structure cont..
• The two chains are antiparallel.
• In the DNA, the Beta-N-glycosidic bonds between
sugar and bases are not directly opposite each other and,
two grooves (major and minor) of unequal width form
around the double helix.
• Rise per nucleotide = 0.33 nm/nucleotide
• Pitch = 3.4 nm / turn
• 10.4 nucleotides per turn
Secondary structure of DNA
 Factors stabilizing the double helix/SECONDARY
STRUCTURE

1. Hydrophobic interactions – burying hydrophobic

purine and pyrimidine rings in interior
2. Stacking interactions – van der Waals interactions
between stacked bases.
3. Hydrogen Bonding – H-bonding between bases
4. Charge-Charge Interactions – Electrostatic
repulsions of negatively charged phosphate
groups are minimized by interaction with cations
(e.g. Mg2+)
 People who contributed to the
discovery of DNA structure
• People who contributed to the discovery of DNA
structure
• Rosalind Franklin and Maurice Wilkins used the
powerful method
• of x-ray diffraction to analyze DNA fibers and They
showed in the early 1950s that DNA produces a
• characteristic x-ray diffraction pattern. Watson and
Crick postulated a three dimensional model of the X-
RAY diffraction pattern. According to three
dimensional structure by Watson and crick postulated
the following:
 According to three dimensional
structure by Watson and crick
postulated the following:
1. Two helical polynucleotide chains are coiled around a common axis. The chains run in opposite
directions.
2. The sugar-phosphate backbones are on the outside and, therefore, the purine and pyrimidine bases lie
on the inside of
the helix.
3. The bases are nearly perpendicular to the helix axis, and adjacent bases are separated by 3.4 Å. The
helical structure
repeats every 34 Å, so there are 10 bases (= 34 Å per repeat/3.4 Å per base) per turn of helix. There is a
rotation of 36
degrees per base (360 degrees per full turn/10 bases per turn).
4. The diameter of the helix is 20 Å.
 RNA MOLECULE
• RNA molecules are less organized compared to DNA.
It is a single stranded molecule with internal hydrogen
bonding to keep it in coiled position. Depending on site
and function, there are four types of RNAs - mRNA,
rRNA, tRNA and viral RNA. The mRNA transfer genetic
information from the nucleus to cytoplasm where
protein synthesis occurs. The rRNA constitutes 85% of
total RNA in the cell and is a constituent of ribosomes,
which is the site for protein synthesis. tRNA delivers
amino acids to the site of protein synthesis. Cells
contain at least one specific tRNA for each of the 20
amino acids found in proteins.
 DIFFERENCE BETWEEN DNA AND RNA
DNA RNA
i) Backbone consists of deoxyribose sugar Backbone consists of ribose sugar
ii) Has bases A, G, C, T,but not U Contain bases A, C, G, U but not T
iii) Has 2 helical strands and are antiparallel Has a single strand
iv) One strand (3’ → 5’) carry (store) genetic information Is informational link between DNA and proteins
vii) DNA is alkali stable RNA is alkali labile
iix) Present in nucleus, mitochondria, chloroplast Present in nucleus and cytoplasm
ix) DNA can form RNA by process of transcription RNA can not give rise to DNA in normal conditions
x) DNA is comparatively a large molecule RNA is comparatively smaller than DNA
 OTHER FUNCTIONS OF NUCLEOTIDES
1. Nucleotide triphosphates have high group potentials,
and participate in many group transfer agents in many
reactions. E.g. ATP, cAMP, GDP, UDP.
2. Many coenzymes are nucleoside derivatives, e.g.
NAD , NADP, FAD, CoASH.
+

3. Nucleotides are poly functional acids and can act as

proton donors or acceptors.
4. Nucleotides are the repeating units in nucleic acids,
i.e. DNA and RNA.