Aspects of Biochemistry

WATER
Specific objective
To discuss how the structure and properties of
water relate to the role that water plays as a
medium of life.
 WATER
Structure
• Water is made up of 2 hydrogen (δ+) atoms and 1 oxygen
_
atom (δ ), and is held together by covalent bonds.
• A covalent bond is a form of chemical bonding that is
characterized by the sharing of pairs of electrons between
atoms
• Water molecules join up with other water molecules by
means of hydrogen bonds.
• Molecules like water that have two separate charged areas
are called dipolar. (polar)
• A hydrogen bond is the attractive interaction
of a hydrogen atom with an electronegative
atom, such as nitrogen, oxygen or fluorine,
that comes from another molecule or
chemical group. The hydrogen must be
covalently bonded to another electronegative
atom to create the bond.
 Water
• The structure of water in being dipolar makes
it an excellent solvent. (dipolar-A molecule
having two such charges or poles)
• Polar and ionic substances e.g. sugar & salt
have electrostatic charge, so they do dissolve
in water. Hydrophilic.
• Non-polar substances, such as oil, have no
charge and do not dissolve in water.
Hydrophobic.
Water dissolving salt
 Properties of water and its biological
significance
Property Significance
• Liquid at room • Provides a liquid environ
temperature. inside cells & aquatic
environ for org. to live in.
• Chemical reactions inside
cells happen in aqueous sol.
Water is also the main
transport medium.
 Properties of water and its biological
significance
Property Significance
• Universal solvent • Chemical reactions inside
cells happen in aqueous sol.
Water is also the main
transport medium
 Properties of water and its biological
significance
Property Significance
• High surface tension • Allows some aquatic organisms such
as pond skaters to land on the
surface of a pond and move about.
E.g. Hunt for food.
• Water molecules have a strong
attraction with each other. However,
on the surface, the uppermost
molecules have other molecules only
below them, not above. So they are
pulled downwards. These pulling
forces draw the molecules closer
together than the other water
molecule resulting in a high surface
tension.
This paper clip is under the water level, which has risen gently and smoothly. Surface tension prevents
the clip from submerging and the water from overflowing the glass edges.
Water molecules below the surface have equal forces acting on them as they are pulled in all directions.
On the surface each water molecule is attracted to other water molecules beside it and below it only and
not above it. This causes the water molecules to be pulled downwards and closer together than in other
parts of the water causing a high surface tension to exist.
Properties of water and its biological significance
Significance
• Ice forms on the surface of a body of water and
Property insulates the water below. This prevents the whole
quantity of water from freezing, hence allowing
• Ice floats on water aquatic life to survive below.
• When water freezes, the molecules slow down. This
causes hydrogen bonding to increase (Max 4) which
results in an increase in volume and a decrease in
density. This results in the formation of a highly
organized geometric pattern called a lattice which
floats on the surface preserving live below.
 Properties of water and its biological
significance
Property
• Water has both cohesive &
adhesive properties.
Significance
• The cohesion and adhesive
properties allow for
capillarity. This is the
movement of water
through narrow spaces. E.g.
Water moves up through
narrow spaces in rocks and
water moving up the xylem
of plants.
Dew drops adhering to a
spider web
 Properties of water and its biological significance
Property
• High specific heat capacity
This deals with the amount of
energy that is required to raising
the temperature of the water.
Significance
• It takes a lot of heat energy to
increase the temp. of water.
• As a result the environment inside
organisms resists temperature
changes.
• Stable aquatic environment.
• The specific heat capacity of water is
4.2Jg-1 ̊C-1
• Applying heat to water causes an
increase in the kinetic energy of the
water molecules which results in an
increase breakage of hydrogen
bonds. Because so much heat is used
to for this, less heat is available to
raise the temperature which accounts
for the high specific heat capacity.
 Properties of water and its biological significance
Property
• High latent heat of vaporization.
(The amt. of heat required to
change a liquid to a gas or from
a gas to a liquid)
Significance
• It takes a lot of heat to convert
water into a gas. The temp. of
water has to be raised to 100 ̊C to
totally change to a gas.
• This property allows for aquatic
organisms to continue living in an
aquatic environment without
having to leave or die.
• Heat is lost from a surface when
water evaporates from it.
• This acts as a cooling mechanism,
for example sweating in mammals
and transpiration in plants.
 Properties of water and its biological
significance
Property Significance
• High latent heat of fusion • Cell content and aquatic
(The amt. of heat required habitats are slow to freeze
to change a solid to a liquid in cold weather.
or a liquid to a solid) To
change water to ice 300J
must be lost for each gram
of water and vice versa.
 Properties of water and its biological
significance
Property Significance

• Pure water is colourless and

transparent.
• Transmission of light
enables aquatic plants to
photosynthesize
 Properties of water and its biological
significance
Property Significance
• Water is difficult to • Supports hydrostatic
compress skeleton in worms,
crustaceans, jellyfish and
turgid plants.
 Properties of water and its biological
significance
Property Significance
• Water takes part in many • E.G. Photosynthesis
chemical reactions. i.e. it is • Many digestive reactions
reactive. such as the breaking down
of food by hydrolysis.
 Aspects of Biochemistry
GLUCOSE
Specific objective
Explain the relationship between the structure and
function of glucose
Explain the relationship between the structure and
function of sucrose
Discuss how the molecular structure of starch,
glycogen and cellulose relate to their function in
living organisms.
 Glucose
• All carbohydrates contain carbon hydrogen and
oxygen. E.g. (sugar, starch, glycogen & cellulose).
• The simplest of sugars is called monosaccharides.
(CH2O)n .
• They are grouped according to the number n.
• Trioses n =3 e.g. Glyceraldehyde, tetroses n = 4
e.g. Threose, pentoses n = 5 e.g. Ribose, hexoses
n=6 e.g. glucose, heptoses n=7 e.g.
Sedoheptulose.
 Glucose
• Glucose is the best known and most abundant
hexose. (C6H12O6).
Aldehyde
group hydroxymethyl
group
 Glucose
• Glucose can take up a number of different
shapes. This phenomenon is called isomerism.
Each isomer has the same chemical formula
but a different structural formula.
• Two main examples are alpha and beta
glucose.
 Glucose
• Examples of other isomers:
Aldehyde Ketone
group group
How is the structure of glucose related to it
function
1) Glucose is highly soluble and metabolically active.
This makes it easy for cells to acquire energy from it
during respiration,
2) The structure of glucose, which has 12 reactive
hydrogens, makes it a good source of energy.

9/6/18
 Glucose
• Two monosaccharides can combine to form a
disaccharide. This is called a condensation
reaction. (Water is lost).
• The bond formed is called an α 1-4 glycosidic
bond.
• The reverse is by a process called hydrolysis
and involves adding water.
α

α α
9/6/18
Equilibrium between cyclic and
open-chain form in one ring of
maltose
Do not have
to learn
 Sucrose

α1-β2

α β
 1 In alpha fructose
the groups on C2
are in opposite to
beta fructose
hence why beta
fructose is used
to form sucrose.

α1-β2
glycosidic bond
 Glucose
• Many monosaccharide units can be added to a
disaccharide in a series of condensation
reactions to form a long chain.
• This chain is known as a polysaccharide.
9/6/18
 Polysaccharide
• Examples of polysaccharide are:
Starch, glycogen and cellulose.
• Starch (energy storage) contains a mixture of two types of
polysaccharides:
Amylose (non-branching) (only α1-4 linkage)
Amylopectin (Branching) ( α1-4 & α1-6)
• Starch is insoluble and metabolically inactive, so it does not
interfere the with water potential or chemical reactions inside
cells. Starch is stored in organelles called plastids.
How is the structure of starch related to its
function
• Starch is insoluble in water and is metabolically inactive, so it
does not interfere the with water potential or chemical
reactions inside cells. This is because starch is stored as starch
granules in the cytoplasm of plant cells. The hydroxylic (-OH)
groups are inaccessible to water in the granule state.
• Secondly, its purpose is to yield energy quickly when needed.
It is able to do that because of it branching nature. Many
enzymes could all work together simultaneously to provide
glucose from it whenever extra energy is needed.

9/6/18
starch
Granules of wheat starch, stained with iodine,
photographed through a light microscope
 Polysaccharide
• Glycogen is found in animals. (Energy storage)
• It contains both α1-4 & α1-6 glycosidic linkages. It is similar to
amylopectin but is more highly branched and less spiral.
• Glycogen is also partially soluble and metabolically
unreactive.
• Because glycogen is highly branched, it allows many enzymes
to act on it simultaneously to yield energy quicker as compare
to amylose and amylopectin.
• This may relate to the fact that most animals have higher
metabolic rates than plants and so may need energy reserves
such as glycogen to be metabolised more rapidly.
 Polysaccharide
• Cellulose is made up of straight chains of β-
glucose only. (Serves as structural building
blocks)
• In order for two β-glucose to form a bond, one
must be rotated at 180° with respect to the
other.
Cellulose
 Polysaccharide
• The hydrogen atoms of –OH groups are weakly attracted to the
oxygen atoms in the same cellulose molecule (the oxygen of the
glucose ring) and also to the oxygen atoms of –OH groups in
neighbouring molecules. This results in a stronger molecule
 Polysaccharide
• Individually these bonds are weak, but so many can form, due
to the large number of –OH groups, that collectively they
develop enormous strength.
 Polysaccharide
• Between 60 – 70 cellulose molecules become tightly cross-linked to form
bundles called microfibrils.
• Microfibrils are in turn held together in bundles called macrofibrils by
hydrogen bonding. Macrofibrils then form cellulose fibers which are also
held together by hydrogen bonds.
 Polysaccharide
• A cell wall typically has several layers of fibers, running in different directions to increase
strength.
• Cellulose fibers have a very high tensile strength, almost equal to that of steel. That means
that if pulled at both ends they are very difficult to break.
• Despite their strength, cellulose fibers are freely permeable, allowing water and solutes to
reach the cell surface membrane.
 Reducing and non reducing sugars
Reducing sugar
• They include sugars that possess a free aldehyde (-CHO) or Ketone (-C=0)
group in their open chain form
• They can reduce the Cu2+ cupric ions (blue)in Fehling’s or Benedict’s
Solution to Cu+ cuprous ions (reddish) that precipitate out as
Cu2O(cuprous oxide).
• E.G. Glucose, maltose, lactose and fructose.
• Non-reducing
• A free aldehyde or ketonic group is lacking.
• No such reaction because the groups is used up in bond formation so it
cannot react.
• E.G. Sucrose and Trehalose (Two alpha glucose molecules linked by a α 1-
1 glycosidic bond)
Oxidation using Benedict's solution
 Lipids
Specific objective
• Describe the molecular structure of a
triglyceride and its role as a source of energy.
• Describe the structure of the phospholipids
and their role in membrane structure and
function
 Lipids
• Lipids are a diverse group of chemicals.
• The most common type is the triglycerides
which are usually known as fats and oils.
 Lipids
• Triglycerides are made by the combination of three fatty
acids (Hydrocarbon tail) and one glycerol molecule (an
alcohol) by condensation reactions. The linkages are
called ester bonds. An ester is a chemical compound
formed by the bonding of an alcohol and one or more
organic acids for example fats.
methyl end
 Lipids
• Triglycerides are insoluble in water but soluble
in certain organic solvent such as ether and
chloroform.
• Triglycerides are non-polar as there is no
uneven distribution of electrical charge. They
are hence hydrophobic .
 Lipids
Saturated and unsaturated fatty acids and lipids.
• Some fatty acids have double bonds between
neighbouring carbons. These are called
unsaturated (<H). (source plants)
• One double bond => monounsaturated
• More than one => polyunsaturated.
• Double bonds make the lipid melt easier & are
the healthy fat.
• Saturated fats have no double bonds, and are
harder to melt and are unhealthy (>H). (source
animals)
Fatty acids E.G. Stearic acid found
in butter
Trans-fatty acids vs. Cis-fatty acids
EA
Less energy
Double
bond
More energy

Single bond

Easier for
enzymes to
access to break
bonds

Trans is latin for “on the opposite

side”
Cis is latin which means “same
side”
 Lipids
Functions
• Excellent energy source.
• Serves as an insulator in mammals
• Lipids are a metabolic source of water for
example in the desert kangaroo rat.
• Important component of cell membranes.
• Lipids are steroids example cholesterol and
testosterone.
 Lipids
Phospholipids
• Phospholipids are a special type of lipid which
are the major component of cell membranes.
• One of the three fatty acids is replaced with a
phosphate group which carries an electrical
charge & therefore dissolves in water. (polar)
• This makes it have a hydrophilic head and two
hydrophobic tails.
 Protein
• Protein is an extremely important class of molecules in living
organisms.
• They have many important functions:
 Essential component of cell membrane
 The oxygen-carrying pigment haemoglobin is a protein
 Antibodies are protein
 All enzymes are protein
 Hair and skin contain the protein keratin
 Collagen from bone and arteries is protein
 Hormones e.g insulin
 Toxins
 Storage (egg white and milk protein)
 Protein
• All proteins are made from the same basis component.
These are amino acids and are the basic building blocks of
protein.
• There are 20 different amino acids found occurring
naturally in living organisms.
• They all have in common a central α carbon to which an
amine group –NH2 , a hydrogen atom, a carboxylic group –
COOH and an R group is attached.
• It is the R group which is also called the side chain group
that varies and give all amino acids their different names.
 Protein
• Basic structure of an amino acid:
9/6/18
-ve +ve
 Proteins
• Two amino acids can join up to form a
dipeptide by means of forming a peptide
bond.
• Any number of extra amino could be added
to the chain in a series of condensation
reaction to form what is called a polypeptide
chain.
Peptide bond formation
 Protein
Primary structure of proteins.

• The types of amino acids contained in the chain, and the

sequence in which they are joined to form a polypeptide
chain is called the primary structure of protein.
• There are enormous number of different possible
primary structures as many different combinations can
be made from the 20 different amino acids.
• Even the change of one amino acid in a chain can have a
significant impact and alter the properties of the
polypeptide of protein.
Primary structure of the enzyme
lysozyme containing 129 amino
acid residues.
Lysozyme catalyses the
breakdown of the cell wall of
bacteria in Phagocytes.
 Protein
Secondary structure
• The primary structure (polypeptide chain) often coils into what
is called an α-helix.
• The helix is held in shape by the formation of hydrogen bonds
between the oxygen of the CO group of one amino acid and the
hydrogen of the NH group of the amino acid four places ahead
of it.
• The hydrogen bonds are strong enough to hold it in shape but
can be easily broken by heat.
• So instead of forming α-helix, they form β-pleated sheets. It all
depends on which R group are present i.e. the type of amino
acids present.
• The polypeptide chain in the a β pleated sheet can either be
parallel or anti-parallel.
Alpha helix
 Protein
Tertiary structure
• In many proteins the secondary structure
folds into a precise three-dimensional shape
known as the tertiary structure.
• The fold is not random as each has its unique
shape and is controlled by genes.
• The folding is as a result of bonding between R
groups.
• Examples include myoglobin, enzymes &
plasma proteins.
Myoglobin (Contains eight α helix regions)
9/6/18
 Tertiary structure
• The tertiary structure in held in shape by five types of
bonds.
 Hydrogen bonds (between R groups and between CO
and NH groups)
 Ionic bonds (b/w R charged groups) E.g asparagine +ev
and glutamic acid –ev.
 Disulphide bonds ( b/w two cysteine molecules)
 Van der Waals forces (b/w R groups that are non-polar)
 Hydrophobic interactions ( non-polar groups repelling
with water) e.g
(Clustering of hydrophobic
groups away from water)
and van der Waals
interactions
 Protein
Quaternary structure.
• In many proteins two or more polypeptide may come
together to form a combined structure called the
quaternary structure.
• Haemoglobin is an example of this, which has four
polypeptide chains. (Two α polypeptides chains and two β
polypeptide chains)
• Haemoglobin is soluble and is found dissolved in the
cytoplasm of RBC.
• They are held in shape by the same five types of bonds as
in the tertiary structure.
• Other examples include insulin and antibodies.
 Globular and fibrous protein
Globular protein
• A protein whose molecules coil up into a ‘ball’
shape, such as enzymes, myoglobin and
haemoglobin, is known as globular proteins.
• Inside cells, proteins are in a fluid environment. E.g.
enzymes
• Globular proteins usually curl up so that their non-
polar hydrophobic side-chains point into the center
of the molecule, away from the watery surroundings.
• The polar hydrophilic side-chains remain on the
outside.
 Globular and fibrous protein
Fibrous protein
• Many proteins do not curl up into a ball, but form long
chains. These are called fibrous proteins.
• Unlike globular proteins, fibrous proteins are usually
insoluble, usually metabolically unreactive and have
structural roles.
• Examples include keratin in hair & skin and collagen.
• Collagen is found in skin, tendons, cartilage, bone, teeth
& blood vessels.
• Collagen consists of three polypeptide chains (each an α
helix) wound around each other in a triple helix, called
tropocollagen that are held together by hydrogen bonds.
 Collagen

One α-helix
chain coiled
in itself into
a loose
helix.

Hydrogen
bonds
 Collagen
• Each complete, three-stranded molecule of collagen
interacts with other collagen molecules running parallel
to it. Bonds form between the R groups of lysines in
molecules lying next to each other. These cross-links
hold many collagen molecules side by side, forming
microfibrils.
• Microfibrils associate to form bundles called fibrils.
Fibrils then associate to form larger bundles called
collagen fibres. Each stage is held together by covalent
bonds.
Collagen
• The ends of the parallel
molecules are
staggered. The
overlapping of these
staggered ends give
collagen its high tensile
strength. If overlapping
was not present,
weak points would
exist in the collagen
molecule making it less
strong.
• Secondly, under
tension, the three
polypeptide strands
interlock like a ‘rope’
and do not unwind
which also accounts for
its high tensile
strength. Covalent
bonds
Collagen
• The Achilles tendon is
the strongest tendon in
the body and can
withstand a pulling
force of 300 N per mm2
• It can withstand a stress
of 3.9 times a persons
body weight when
walking.
 Conjugated proteins
•A conjugated protein is a that functions in interaction with other chemical
groups attached by or by weak interactions.
•Many proteins contain only and no other chemical groups, and they are called
simple proteins. However, other kinds of protein yield, on hydrolysis, some other
chemical component in addition to amino acids and they are called conjugated
proteins. The non-amino part of a conjugated protein is usually called its . Most
are formed from vitamins. Conjugated proteins are classified on the basis of the
chemical nature of their prosthetic groups.
•Some examples of conjugated proteins are , , , , , and .
• contains the containing iron, which is the . 1 Oxygen molecules bind to the
iron ion (Fe2+) found in the group.
•Glycoproteins are generally the largest and most abundant group of conjugated
proteins.