ASPECTS OF BIOCHEMISTRY

 BIOMOLECULES:
 WATER

 CARBOHYDRATES: Monosaccharides,
Disaccharides, Polysaccharides
 LIPIDS: Triglycerides, Phospholipids

 PROTEINS
BIOMOLECULES

 Molecules made by living organisms

 Many biomolecules are MACROMOLECULES,
large molecules that are composed of smaller
subunits.
 Some macromolecules are POLYMERS, that is,
the subunits that make up the molecule are similar
or exactly the same one to the other.
 Other biomolecules are very simple, such as water.
WATER
 WATER
 2 HYDROGEN + 1 OXYGEN
 SMALL, POLAR
 EACH WATER MOLECULE HAS A WEAK
ATTRACTION TO ANOTHER
 FORMS HYDROGEN BONDS(H-BONDS)
 INDIVIDUAL H-BONDS ARE WEAK BUT
THEIR COLLECTIVE EFFECT IS
RESPONSIBLE FOR ALL THE
PROPERTIES OF WATER
 The oxygen atom is more electronegative than the
hydrogen atoms so the shared electrons orbit the O
more than they do the H.
 A slightly negative charge is thus conferred onto the
O and a slightly positive charge to the H.
 A molecule or atom that possesses a charge is
described as being polar.
 A water molecule has two charges and so is dipolar.
 The presence of charges makes water molecules
attracted to other charged or neutral molecules.
 Water molecules are attracted to each other, forming
hydrogen bonds.
 A hydrogen bond is a weak attraction that is formed
between a hydrogen atom that is covalently bonded
to a more electronegative atom (which makes the H
slightly positive in charge) and another negatively
charged atom.
 Each water molecule can form a maximum of
FOUR hydrogen bonds.
 Hydrogen bonds are represented by broken lines.
 IMPORTANCE OF WATER
 Is a constituent of all living cells(70-95%).
 All biochemical processes occur in water. In many
cases water makes reactions possible.
 Provides a home for aquatic organisms.
 Is a solvent for polar, neutral and ionic substances.
Its solvent properties allows blood to transport a
wide range of chemicals.
 The lymphatic, osmoregulatory, excretory and
digestive systems of animals need water to operate.
 Water is also a necessary support medium for some
plants and animals. Some animals have hydrostatic
skeletons (Sponges, worms); plant cells store water
to help the plant keep its shape and form.
 Needed in fertilization as it provides the base for the
fluid in which gametes move.
 Serves a protective function as well. For instance
tears help to kill potential bacteria.
 Provides lubrication at joints.
 Is essential to transport in plants.
PROPERTIES OF WATER AND THEIR IMPORTANCE TO LIFE
PROPERTY
HIGH HEAT CAPACITY- it takes a large
amount of energy to raise the temperature of
water. Most of the heat energy is used to break
the hydrogen bonds so temperature change is
minimal.
HEAT CAPACITY IS THE AMOUNT OF
ENERGY NEEDED TO RAISE THE
TEMPERATURE OF A LIQUID BY 1
degree Celsius.
HIGH HEAT OF VAPORIZATION- water
has a very high boiling point for such a small
molecule. It takes a huge amount of energy to
convert liquid water to its gaseous form.
Heat of vaporization is the amount of energy
needed to convert a liquid to gas.
DENSITY AND FREEZING- as temperature
lowers, water‘s density increases until 4
degrees C. Below this temperature, its density
decreases so that ice is less dense than liquid
water.
IMPORTANCE
Biochemical processes operate over a small
temperature range. Temperature must be
relatively constant for successful reactions.
Reactions are inhibited by extremes in
temperature.
Aquatic organisms have a constant home
environment in which to live.
Ensures constant presence of liquid water on
Earth. The water is not all vaporized by the
intense heat of the sun.
Allows animals to remove lots of heat, by
sweating and panting, with minimal water loss.
Bodies of water (ponds, lakes, seas, oceans
etc) will not freeze solid. Aquatic organisms
are thus not deprived of a home nor killed off.
The top layer of ice insulates the water below
it.
 PROPERTY
HIGH SURFACE TENSION AND
COHESION- individual water molecules stick
together (cohesion) due to their H-bonds. This
results in the formation of a ‘film’ at the water-
air interface(surface tension).
Surface tension is the difficulty involved in
breaking the surface of a liquid
REAGENT- water takes part in some
chemical reactions.
SOLVENT- water is described as the universal
solvent. This is because of the wide array of
substances that can be dissolved in water. This
involves polar, neutral and ionic substances.
IMPORTANCE
Cohesion is important for transport of water
and organic substances in plants. It allows
material to be moved against gravity.
Some animals (pondskater, basilisk lizard) can
stand, walk or run on water. This aids in their
escape from predators and/or capture of prey.
Photosynthesis is the basic reaction that
supports almost all life on Earth.
Hydrolysis reactions aid in the breakdown of
complex molecules.
Important molecules are able to dissolve in
blood and so be transported around the body.
Hormones, ions, proteins are a few.
Furthermore, ions dissolve in water inside of
cells and in so doing are able to participate in
chemical reactions.
Sugars, hormones and other chemicals are also
moved in plants’ cell sap because they are
dissolved in water.
 MACROMOLECULES
 CARBOHYDRATES
 TRIGLYCERIDES
 PHOSPHOLIPIDS
 PROTEINS
 Carbohydrates and proteins are polymers, that is
they are made from many identical or similar
repeating smaller units.
 Because these macromolecules are made by living
cells, they are called biomolecules.
CARBOHYDRATES
 Hydrates of carbon with the general formula
Cx(H2O)y
 Monosaccaharides are the simplest carbs. They
consist of just one sugar molecule.
 Disaccharides possess two sugar molecules.
 Polysaccharides have many sugar molecules.
MONOSACCHARIDES
 Formula : (CH2O)n

 Number of carbons range from three to seven

with hexoses being the most common.
 Includes glucose, fructose, ribose and galactose
 Forms ring structures
 The most common monosaccharide is glucose
GLUCOSE C6H12O6
ALPHA GLUCOSE
BETA GLUCOSE
 Glucose functions as an energy source when oxidised
in respiration.
 It is well suited to this function because its simplicity
makes it easy to breakdown quickly.
 Also its most reactive group, the hydroxyl group on
carbon 1, is free to engage in reactions.
 As a simple sugar it is easily converted to larger
carbohydrates for storage.
 GLUCOSE, FRUCTOSE and GALACTOSE ARE
STRUCTURAL ISOMERS.
 THEY HAVE THE SAME MOLECULAR
FORMULA BUT DIFFERENT STRUCTURAL
FORMULAS.
 Glucose forms a six sided ring while fructose forms
a 5 sided ring.
 DISACCHARIDES C12H22O11

 Formed when two monosaccharides are joined.

 The bond between two monosaccharides is called a
glycosidic bond or linkage.
 There are different types of glycosidic bonds
depending on which carbon atoms are involved.
 The most abundant disaccharide is sucrose.
 Glucose and fructose undergo a condensation
reaction to form the disaccharide sucrose.
 A condensation reaction is one that results in the
formation of water as a by-product.

 Sucrose is the food transport molecule in plants.
 Glucose is converted to sucrose and is in this way
moved from the leaf to other parts of the plant.
 Sucrose is relatively unreactive because the OH on
C-1 is locked in a bond, so it wont get involved in
reactions as it is moved.
 It is also soluble so it can dissolve in water and be
transported.
 Sucrose is not too complex so it is easily hydrolysed
to its constituent monomers at the required areas.
SUCROSE
The OH groups of carbon1 of the Glucose and carbon
2 of the Fructose undergo condensation thereby
forming a 1,2 glycosidic bond in sucrose
DISACCHARIDES
 Another disaccharide is maltose.
 It is formed from two alpha glucose molecules
 The bond between the two molecules is a 1, 4
glycosidic linkage.
 The glycosidic bond in sucrose is…?
 Lactose, another disaccharide, is formed from the
bonding of glucose and galactose.
The OH groups on carbon 1 of one glucose and carbon 4 of the other
glucose undergo condensation thereby forming a 1,4 glycosidic link in
maltose
 POLYSACCHARIDES
 The largest carbohydrates.
 Formed from many monosaccharides joined by
glycosidic bonds.
 Polysaccharides are polymers; that is, they are
comprised of many similar or identical repeating
subunits called monomers.
 Different polysaccharides will have different
monomer units.
 Three polysaccharides are: starch, cellulose and
glycogen.
 STARCH:

 Long chains of alpha glucose units

 From a few hundred to the thousands
 Most units are linked to another by alpha 1,4
glycosidic bonds.
 A smaller number of glucose units are linked by
alpha 1,6 glycosidic bonds.
 3 D structure is an alpha helix
 There are two types of starch: (i) AMYLOSE
(ii) AMYLOPECTIN
FORMATION OF STARCH
 AMYLOSE

•STRAIGHT CHAINS OF ALPHA GLUCOSE

UNITS
LINKED BY 1,4 GLYCOSIDIC BONDS
•DOES NOT CONTAIN ANY BRANCHES
•FORMS A BLUE-BLACK COLOUR WITH
AMYLOPECTIN
AMYLOPECTIN
 BRANCHED CHAINS OF ALPHA GLUCOSE UNITS

 UNITS ON THE STRAIGHT CHAINS ARE LINKED

BY 1,4 GLYCOSIDIC BONDS WHILE THE
BRANCHES ARE FORMED BY 1, 6 GLYCOSIDIC
BONDS BETWEEN GLUCOSE UNITS

 FORMS A PURPLE BLUE COLOUR WITH IODINE

 STARCH
 Functions as the food storage molecule in plants.
 Starch’s structure supports this function well:
1. the OH groups are hidden on the inside of the
helix thereby making the molecule unreactive.
2. the helical structure reduces the amount of space
the molecule takes up.
3. Its large size makes it insoluble and this ensures
that it is kept in its storage place and that it doesn’t
interfere with the plant’s osmotic balance.
 CELLULOSE
 Long chains of beta glucose molecules linked
by beta 1,4 glycosidic bonds.
 Does not form a helix; chains are straight.
 Neighbouring chains connect together by
hydrogen bonds.
 A group of about 60-70 chains form a
microfibril.
 A group of microfibrils form a macrofibril.
 Macrofibrils are arranged in layers.
 Cellulose function is to provide structural support
for plants. It possesses great tensile strength.
 It is the cumulative effect of thousands of hydrogen
bonds that confers this strength to cellulose.
 Plant cells are wrapped in several layers of cellulose
(macrofibril) that forms their cell wall.
 It is the cellulose that prevents plant cells from
bursting when they take in water.
 Turgidity is important for plants that do not contain
wood to remain upright.
 At the same time cellulose is completely permeable
to water and solutes.
GLYCOGEN
 Composed of alpha glucose molecules.
 Is the food storage molecule in animals. It is
stored in the liver and muscle cells.
 Is very similar in structure to amylopectin except
that glycogen is more extensively branched and
the average chain length is much longer.
 Glycogen is more soluble in water than starch is.
 All the features that make starch a good storage
molecule (helical shape, unreactivity, etc) applies to
glycogen as well, making it a good storage molecule
too.
 Furthermore, the increased branching of glycogen
opens up the molecule more than starch making it
more soluble and more easily broken down.
 This is important as animals often need quick bursts
of energy and the fast conversion of glycogen
allows this.
 TRIGLYCERIDES
 A macromolecule but NOT a polymer
 Comprised of one glycerol molecule bonded to three
fatty acids.
 Glycerol is a 3 carbon alcohol with three hydroxyl
(OH) groups.
 A fatty acid is a long chain of carbon and hydrogen
(hydrocarbon)possessing a carboxyl group (COOH)
at one end.
 Fatty acids usually have between 16 to 22 carbons.
 A condensation reaction occurs between the 3
hydroxyl groups of glycerol and the carboxyl groups
of 3 fatty acids.
 Each bond is called an ESTER BOND. So there are 3
ester bonds in a triglyceride.
 Triglycerides are either fats or oils.
 Fats are solid at room temperature; they contain
mostly saturated fatty acids.
 Oils are liquid at room temperature; they possess more
unsaturated fatty acids.
 Fats and oils serve as energy stores in animals and
plants respectively.
 Other functions include insulation and protection of
TRIGLYCERIDE FORMATION
A DETAILED TRIGLYCERIDE
FATTY ACID TAILS MAY BE REPRESENTED USING A CAPITAL ‘R’
AND SUBSCRIPTING 1, 2 AND 3 RESPECTIVELY FOR EACH
THE TAILS MAY ALSO BE REPRESENTED AS A ZIG-ZAG LINE
WHERE EVERY JUNCTION OR ‘POINT’ IS A CARBON ATOM
 Triglycerides are non-polar and hydrophobic. They
are insoluble in water.
 These properties are due to the long hydrocarbon
tails.
 Saturated fatty acids have the full number of
hydrogens possible on each carbon in the chain.
 Unsaturated fatty acids have one or more multiple
bonds between carbons in the chain so these carbons
have less H than normally possible.
 The multiple bonds in unsaturated fatty acids makes
the molecules unable to pack uniformly and so is
hard to solidify.
 Triglycerides are good storage molecules because:
1. They are insoluble in water which allows them to be
deposited at specific locations in an organism
2. Triglycerides have higher caloric value than
carbohydrates. This means that they yield more
energy per gram than carbs.
3. Triglycerides are lighter than carbohydrates. This is
particularly important for mobile organisms.
 Fats are so much better as a storage molecule that
animals store fats in preference to glycogen resulting
in organisms becoming overweight.
 Animals living in cold areas accumulate more
unsaturated triglycerides since this prevents them
 PHOSPHOLIPIDS
 A macromolecule but NOT a polymer.
 Comprised of one glycerol, two fatty acids and one
phosphate group.
 The fatty acids and phosphate group are linked to
the glycerol by ester bonds.
 The phosphate group is polar, having a negative
electrical charge and is therefore hydrophilic.
 The fatty acids are non polar and hydrophobic.
 A phospholipid thus has a polar phosphate head and
two non polar hydrocarbon tails.
PHOSPHOLIPID
 In water phospholipids’ hydrophobic tails aggregate away
from the water and the hydrophilic head interacts with the
water resulting in a structure called a micelle.
 Micelles are important in the transport of lipids out of the
intestines into blood and into cells.
 More importantly, phospholipids form the core of all
biological membranes.
 The heads face the aqueous environment inside and
outside cells and the tails aggregate together forming two
layers of tails facing each other.
 This is called the lipid bilayer.
 The phospholipid bilayer forms the boundary between a
cell and its external environment.
MICELLE
LIPID BILAYER OF MEMBRANES
 The phosphate confers polarity and thus
hydrophilic behaviour while the hydrocarbon
tails confer non polarity and hydrophobic
behaviour.
 As such, this one molecule having both
hydrophobic and hydrophilic features, allows for
the arrangement of a bilayer and the functionality
of all membrane systems.
PROTEINS
 Macromolecules that make up 50% of the dry
weight of most cells.
 Polymers of amino acids.
 AMINO ACIDS
 The monomer unit of proteins.
 An amino acid consists of an asymmetrical carbon
bonded to: an amino group, a hydrogen, an R group,
and a carboxyl group.
 There are 20 different essential amino acids.
 Proteins are formed by bonding amino acids together.
The bond between amino acids is called a peptide
bond.
 A peptide bond is formed by condensation reaction
between the amino group of one amino acid and the
carboxyl group of another.
 Many amino acids joined together form a polypeptide.
GENERAL STRUCTURE OF AN AMINO ACID
IN AQUEOUS SOLUTION THE CARBOXYL GROUP LOSES A HYDROGEN
TO THE MORE ELECTRONEGATIVE NITROGEN OF THE AMINO GROUP
PEPTIDE BOND FORMATION
THERE IS A REPEATING SEQUENCE PRESENT IN THE POLYPEPTIDE CHAIN REFERRED
TO AS THE POLYPEPTIDE BACKBONE.
THIS SEQUENCE IS N-C-C-N-C-C-N-C….
 Amino acids’ R groups project from this backbone
and as such are called side chains.
 An R group can be as simple as a hydrogen atom as
in the case of glycine or complex ring or chain
structures.
 An amino acid’s properties are defined by its R
Group since the R group is the only thing that
differentiates one amino acid from another.
 So individual amino acids may be acidic, basic,
polar, non polar, hydrophobic or hydrophilic based
on the R group present on it.
 There are FOUR levels of protein structure.
 LEVELS OF PROTEIN STRUCTURE
 Primary Structure: the unique sequence of amino
acids, joined by peptide bonds, in the polypeptide chain.
The order in which the amino acids occur.
 Each protein has its special sequence of amino acids.
 This sequence is specified by instructions in a gene, the
cell’s DNA. Using analytical methods investigators can
determine the exact sequence of amino acids in a protein
molecule.
 The protein hormone glucagon is a small polypeptide
consisting of 29 amino acids.
 If a single amino acid is missing, the protein function is
disturbed.
PRIMARY STRUCTURE OF GLUCAGON
 Secondary Structure: the coiling or folding of the
polypeptide into sheets or helices is referred to the
protein’s secondary structure.
 These coils and folds are the result of hydrogen
bonds between the repeating constituents of the
polypeptide backbone (not the amino acid side
chains).
 Both the oxygen and the nitrogen atoms of the
backbone are electronegative, with partial negative
charges. The weakly positive hydrogen atom
attached to the nitrogen atom has an affinity for the
oxygen atom of a nearby peptide bond and thus
forms a hydrogen bond with it.
 Individually, these hydrogen bonds are weak but
because they are repeated many times over a
relatively long region of the polypeptide chain, they
can support a particular shape for that part of the
protein.
 Two most common types of secondary structure are
the α helix and the β- pleated sheet.
 Alpha helix or beta pleated sheet are the basic forms
of secondary structure. They can exist separately or
jointly in a protein.
 ALPHA HELIX
 An alpha helix is a region where a polypeptide chain
forms a uniform helical coil; an extended spiral
spring.
 The helical structure is determined and maintained
by the formation of hydrogen bonds between
successive turns of the spiral coil.
 The partial positive H atom of the amino group of
one amino acid is bonded to the partial negative O
atom of the carboxyl group four amino acids away.
 So amino acid 1 is bonded to amino acid 5 and
amino acid 2 to 6 etc
ALPHA HELIX
 BETA PLEATED SHEET
 The other main type of secondary structure is the
beta pleated sheet. The hydrogen bonding in this
sheet takes place between different polypeptide
chains; the chains lying side by side or between
different regions of a polypeptide that has turned
back on its self. The polypeptide chains that are
bonded, line up parallel beside each other.
 Each chain is fully extended, but because each has a
zig zag structure the resulting sheet has an overall
pleated formation (Much like a sheet of paper that
has been folded into a fan).
BETA SHEET
 Tertiary Structure: The folding back of the
polypeptide upon itself held together by disulfide
bridges, hydrogen and ionic bonds or hydrophobic
interactions to form a precise 3-D shape.
 This 3-D structure is determined and maintained by
the above mentioned four interactions among R-
groups belonging to the same polypeptide.
 The tertiary structure is laid down ‘on top of’ the
primary and secondary structures.
 The four interactions that govern the tertiary
structure are:
1. Hydrogen bonds form between an R group with a
positive H and another with an electronegative atom.
2. An ionic bond can occur between an R group with a unit
of positive charge and another with a unit of negative
charge.
3. Hydrophobic interactions result from the tendency of
non polar R groups to be excluded by the surrounding
water and therefore to associate in the interior of the
protein.
4. Covalent bonds known as disulphide bonds may link
the sulphur atoms of two cysteine subunits belonging to
the same chain. A disulfide bridge forms when the
sulfhydryl groups of two cysteines react, the two
hydrogen are removed and the two sulfur atoms that
 Quaternary Structure: Complex structure formed
by the interaction of 2 or more polypeptide chains.
 Many functional proteins are composed of two or
more polypeptide chains, interacting in specific
ways to form the biologically active molecule.
 The quaternary structure is the resulting 3-D
architecture of these polypeptide chains, each with
its own primary, secondary and tertiary structure.
 The same types of interactions that produce
secondary and tertiary structure also contributes to
quaternary structure.
 Not all proteins have a quaternary structure.
 There is much more to be said on the topic of
proteins which will be addressed shortly.
 BIOCHEMICAL REACTIONS
 Disaccharides, polysaccharides, triglycerides,
phospholipids and proteins are formed from
condensation reactions.
 Alpha Glucose + Alpha glucose = Maltose + Water
 Amino Acid + Amino Acid = Dipeptide + Water
 Glycerol + 3 Fatty Acids = Triglyceride + 3 Water

 In all cases water is liberated. Of course the

number of water molecules vary according to the
molecule being formed.
 A condensation reaction can be reversed by the
addition of water.
 A reaction in which water is a reagent is called a
Hydrolysis reaction. Hydrolysis reactions reverse
condensation reactions.
 So the monomer units of disaccharides,
polysaccharides, triglycerides, phospholipids and
proteins can be obtained by adding water to these
biomolecules. Enzymes facilitate the process.
 Starch + ≈Water = Alpha Glucose Units
 Sucrose + Water = Glucose + Fructose
 Protein + ≈Water = Amino Acids
 Phospholipid + 3 Water = 1 glycerol + 2 fatty acids +
Condensation:
C6H12O6+ C6H12O6 = C12H22O11 + H2O

Hydrolysis:
C36H62O31 + 5 H2O = 6 C6H12O6