1

Properties of Water
2.1.2(a)
Keywords: Cohesion, adhesion

Learning Objectives:

• Describe how hydrogen bonds occur between water

molecules
• Explain how properties of water allow organisms to survive in
a range of temperatures:
 Solvent – some
Reactant in lots of substances dissolve in
chemical reactions. it. Most biological
Including hydrolysis reactions take place in
solution (in cytoplasm)

The Transports substances

Ice floats
Water is less dense importance Like glucose and
oxygen around plants
when it is a solid and
forms an insulating of Water and animals
layer

Temperature control
- High specific heat
capacity and high
Habitat
latent heat of
Organisms survive and
evaporation
reproduce in it
 Water
A water molecule (H2O), is made up of three atoms -
one oxygen and two hydrogen.

60 – 70 % of mammals
About 90% of plants
Life originated in water
Representing a water molecule

H2 O
 Water is Polar
In each water molecule, the oxygen
atom attracts more than its "fair
share" of electrons.

The oxygen end “acts” negative

The hydrogen end “acts” positive

This causes the water to be POLAR

(has both positive and negative).

However, water is neutral (equal

number of e- and p+) --- Zero Net
Charge.
 Hydrogen Bonds Exist Between Water Molecules
Formed between a highly electro-negative atom of a polar
molecule and a hydrogen

One hydrogen bond is weak, but many hydrogen bonds are strong
What are the
Properties of
Water?
 Properties of Water
Cohesion
Adhesion
High Specific Heat
High Latent Heat of Vaporisation
Density
Solvent
Cohesion …

Produces a surface film on water that

allows insects to walk on the surface of
water.
 Cohesion
Attraction between molecules of the
same type due to polarity of the
molecule
Results in surface tension (a measure of
the strength necessary to stretch or
break the surface of a liquid’s surface).

Water has a greater surface

tension than most other liquids
because hydrogen bonds among
surface water molecules resist
stretching or breaking the surface.
 Adhesion
Attraction between two
different substances.

Water will make hydrogen bonds

with other surfaces.

Example: transpiration process

which plants and trees remove
water from the soil, and paper
towels soak up water.
Demo
Adhesion Also Causes Water to …

Attach to a spider
Form spheres & web
hold onto plant
leaves
 Specific heat capacity
The energy needed to raise 1kg of water by 1oC

Due to H bonds, water can absorb or release large

amounts of heat energy with little change in actual
temperature.
 Water as a habitat
The water serves as a large heat sink responsible for:
1.Prevention of temperature fluctuations that are
outside the range suitable for life.
2. A stable marine environment
 High Latent Heat of Vaporisation
Amount of energy to convert 1Kg of a substance from a
liquid to a gas
In order for water to evaporate, hydrogen bonds must be
broken. As water evaporates, it removes a lot of heat with
it (cooling effect).

This is responsible for:

Moderating earth’s
climate

Preventing organisms
from overheating
 Density of Water
The density of water:
1. Prevents water from freezing from the bottom up.
2. Ice forms on the surface first—the freezing of the
water releases heat to the water below creating
insulation.
3. Makes transition between season less abrupt.

Most dense at 4oC

Contracts until 4oC
Expands from 4oC to 0oC
 Water is Less Dense as a Solid
Ice is less dense as a solid than as a liquid (ice floats).
Liquid water has H bonds that are constantly being
broken and reformed.
Frozen water forms a crystal-like lattice whereby
molecules are set at fixed distances.
Which is ice and which is water?
Which is ice and which is water?

Wate Ice
r
Water as a solvent
 Solvent for Life
Water is a good solvent for many
substances.

As water is polar, the positive and

negative parts are attracted to the
negative and positive parts of a
solute.

The water molecules cluster around

the solute molecules and keep
them apart. As water is a good solvent,
molecules and ions can be
transported around living things
At this point, they dissolve and a whilst dissolved and reaction can
solution is formed. occur.
6 mark Exam
Question
high latent heat of vaporisation / large amount water (beneath ice), insulated / remains
of energy required to change from liquid to gas liquid / doesn’t freeze

evaporation is (efficient) cooling mechanism (aquatic) organisms, do not freeze / can still
swim ;
example of cooling in living organism
(effective) solvent ;
high specific heat capacity / large amount of medium for reactions / (internal) transport
energy needed to, raise / change, temperature medium / able to dilute toxic substances

(thermally) stable environment for, aquatic cohesion / adhesion ;

organisms
example of cohesion / adhesion, in living
(aquatic) organisms use less energy on organism ;
temperature control
surface tension ;
(internal) temperature of organisms changes habitat for (named) invertebrates ;
only slowly (biological) reactions / enzymes /
metabolism, function(s) correctly idea of high density ;
allows flotation / support ;
ice, is less dense than water / floats

(surface of) ice provides habitat for, organisms

2
Molecular bonding
2.1.2(b and c)
Keywords: condensation, hydrolysis

Learning Objectives:
• Recall covalent bonding from GCSE
• Describe the concept of monomers and polymers
• Explain the difference between condensation and
hydrolysis reactions
Remember GCSE chemistry

Draw the electron structure of

a carbon atom

Ext. How many

protons, how many
neutrons?
Covalent bonding
Atoms consist of a nucleus (protons
and neutrons), surrounded by
electrons.

Most atoms are stable when their

outer most shells are full.

Carbon has 4 electrons in it’s outer

shell, so by sharing electrons with
other atoms, the outer most shells
can be ‘filled’. This is an example of
covalent bonding.
Remember GCSE chemistry

Draw the covalent bonding for

methane CH4 and Water H2O

Ext. try O2 and N2

 Covalent bonding

Methane Water
 Monomers and Polymers
A monomer is a single unit.

If many monomers are joined together you

make a polymer.
 Condensation and hydrolysis
A condensation
reaction occurs
when 2 molecules Molecule Molecule
OH HO
are joined 1 2
together with the
removal of water.
H20 is added H20 is removed

A hydrolysis
reaction uses O
water to split the
molecules apart. Molecule 3
 Condensation

Glycosidic bond
α α
 Hydrolysis

Maltose Glucose Glucose

Condensation

Sucrose
 Condensation
Esterification (Chemistry example)

methanol butanoic acid

methyl butanoate water

 Condensation

Amino acid 1 Amino acid 2

Dipeptide + water

When two amino acids combine in a condensation reaction, a covalent bond forms between
the amine nitrogen of one amino acid and the carboxyl carbon of the second amino acid. It
forms a dipeptide and a molecule of water is then removed as a second product.
 Monomers and polymers
Condensation and hydrolysis reactions are responsible for linking
and splitting apart biological molecules.
Units which are joined together are called monomers and form a
dimer. Lots of monomers joined together are called polymers.
Type of molecule Made up of Monomer Polymer
Carbohydrates (C, H and O) Monosaccharid Polysaccharides
es (e.g. (e.g. starch)
glucose)
Proteins (C, H, O, N Amino acids Polypeptides
and S) and proteins
Nucleic acids (C, H, O, N Nucleotides DNA and RNA
and P)
Lipids (C, H and O)
3
Carbohydrates
2.1.2(d and e)
Keywords: monosaccharide, disaccharide, polysaccharide

Learning Objectives:

• Describe the ring structure and properties of glucose as

an example of a hexose monosaccharide and the
structure of ribose as an example of a pentose
monosaccharide
• Describe the synthesis and breakdown of a disaccharide
by the formation and breakage of glycosidic bonds
 Carbohydrates
Contain the elements C, H and O (CH2O) – ‘hydrated carbons’
Uses of carbohydrates
• Substrate for respiration(glucose)
• energy store ( starch and glycogen)
• Structural - cellulose, chitin in arthropod exoskeletons and
fungal walls
• Hereditary information – pentose sugar (deoxyribose
• Recognition of molecules outside a cell (e.g. attached to
proteins or lipids on cell surface membrane).
 Monosaccharides
The carbon backbone can be made of
3, 4, 5 or 6 carbon atoms,
• one C forms a double bond with
an oxygen atom
• the other carbons in the chain are
bonded to one hydrogen atom (H)
and one hydroxyl group (- OH).

They are sugars which taste sweet

and are soluble in water.
The simplest monosaccharide is the 3-carbon compound glyceraldehyde.
The 5 and 6 carbon monosaccharides are the most important biologically.

triose pentose hexose

 Glucose occurs more commonly in the ring configuration when in
solution where the carbon atom 1 (1C) joins to the O on (5C).

H 1
O 6
CH2OH
C
H 2
C OH 5
C
H O H
3 H
OH C H 4 1
C OH H C
4
H C OH
3
5 OH OH C 2
C OH
H C
6 H
CH2OH OH
Chain for a glucose α-glucose ring form
Making the drawing easier

H
O

OH
Spot the difference
 Isomerism
In solution, glucose can take up
a number of different shapes.

This is called isomerism.

Each isomer has the same

chemical formula but a They differ only in the position of the
different hydroxyl group on carbon 1
structural formula. The most
common glucose isomers are:

α & β glucose
 Disaccharides
Formed from two monosaccharides joined by a
glycosidic bond during a condensation reaction:
 Disaccharides
glucose + glucose maltose (malt sugar)
glucose + galactose lactose (milk sugar)
glucose + fructose sucrose (table sugar)
 Condensation

To form a dimer
Monomers can be
such as maltose, or
joined togther
any other polymer...

A disaccharide 1,4 glycosidic bond

 Hydrolysis

A dimer such as ...can be broken apart

maltose, or any into its constituent
other polymer... monomers.
4
Carbohydrates – polysaccharides
2.1.2(e and f)
Keywords: amylopectin, cellulose

Learning Objectives:

• Describe the synthesis and breakdown of a

polysaccharide by the formation and breakage of
glycosidic bonds
• Compare the structure of starch (amylose and
amylopectin), glycogen and cellulose
glucose fructose sucrose

What is the name of the reaction to create this glycosidic

linkage between the two sugars?
condensation

What is the scientific term for a pair of monomers linked

together?
disaccharide
 Polysaccharides
Linkages between many sugar molecules create complex
carbohydrates.
Three important examples:
– Starch
– Glycogen
– Cellulose

What is the scientific term for

many monomers linked
together?
 Starch
• Plants store excess glucose as starch
• Insoluble in water so doesn’t affect osmosis
• Mixture of amylose and amylopectin
– Amylose is a long unbranched chain of α glucose, has a
compact coiled structure good for storage
– Amylopectin long branched chain of α glucose. Glucose
can be released quickly as it is easier for enzymes to get to
the branches.
Amylose Amylopectin
 Glycogen
• Animals store excess glucose as glycogen in the liver
and muscles
• Polysaccharide of α glucose
• Has lots of side branches excellent for fast release of
energy
• Compact and good for storage
Comparison of amylopectin and glycogen.
 Cellulose
• Long straight unbranched chains of β glucose
• Hydrogen bonds form between the chains forming
strong fibres called microfibrils
• Structural support for cells e.g. plant cell wall
 Cellulose
Cellulose is made up of β 1-4 glucose molecules. Each alternate glucose
molecule flips 180° to allow the bonding of the hydroxyl groups. This means
that the CH2OH alcohol group of every other molecule is above the carbon
ring, and the others are below.
 Cellulose structure

Many chains run parallel to each other forming microfibrils and are
strengthened with cross- linkages (hydrogen bonds) between them.
This gives cellulose its stability and a valuable structural material. This
stability of cellulose makes it difficult to digest.
 Structure and function of
plant cell walls

Cellulose microfibrils are

embedded in a framework of other
substances, the most common
being hemicellulose and pectins.

This gives the strength to support

the cell wall.

There is also space between the

fibrils to allow water and mineral
ions to pass through, however, in
some cases these gaps are blocked
(suberin) to make it waterproof.
Compare the structure of starch,
glycogen and cellulose

Ext. List the functions of carbohydrates

 Comparison of starch, glycogen and cellulose

Starch and Glycogen Cellulose

α glycosidic bonds β glycosidic bonds
flexible chains straight chains
H bonds within each chain, H bonds between chains,
forming helix forming microfibrils
Can form H-bonds with water, Can't form H bonds with water,
so can be soluble so insoluble
Reacts with iodine to form Doesn't react with iodine
purple complex
Easy to digest Difficult to digest
Storage role Structural role
 Quick quiz
1. What is the structural difference between alpha-glucose and
beta glucose?
For alpha on 1C the OH is at the bottom and H on the top. This is reversed for beta
2. Describe how glycosidic bonds are formed
During a condensation reaction, water is removed leaving –O-
3. Describe the structure of starch
Mixture of 2 alpha-glucose polysaccharides. Amylose (coiled) and
amylopectin(branched)
4. What is the function of cellulose?
Provide structural support for cells e.g. plant cell wall

5. State the function of glycogen and explain how its structure

is related to its function.
Polysaccharide of beta-glucose
Stores excess glucose in animals
Branched structure means glucose can be released quickly
Compact – good for storage
5
Lipids - triglycerides
2.1.2(h and i)
Keywords: glycerol, fatty acids

Learning Objectives:

• Describe the structure of a triglyceride

• Describe the synthesis and breakdown of triglycerides
by the formation and breakage of ester bonds
between fatty acids and glycerol
 Introduction to lipids
Lipids contain large amounts of
C and H and smaller
amounts of O.

Insoluble in water as they are not

polar

The three most important lipids

are
• triglycerides (fats and oils),
• phospholipids
• steroids.

Not polymers, but are made of

different components and
examples of macromolecules.
 Triglycerides
• Triglycerides are
macromolecules
• Contain C, H and O
• One molecule of glycerol
and 3 fatty acids
 Functions of triglycerides
• Energy source – triglycerides are broken down in respiration to
release energy and generate ATP.

• Energy store – as triglycerides are insoluble in water, they can

be stored without affecting the water potential of cells.

• Insulation – lipid around nerve cells act as an electrical

insulator

• Buoyancy – fat is less dense than water so is used by aquatic

mammals to help them stay afloat

• Protection – fat around organs act as a shock absorber

 Glycerol
A molecule of glycerol is
made up of three carbon
atoms.

Each of these has a

hydroxyl group attached to it.

Hydrogen atoms occupy the

remaining positions.
 Fatty Acids
A single fatty acid molecule
contains an acid (COOH)
group attached to a
hydrocarbon chain.

The hydrocarbon chain can be

from 2 to 20 carbons long.
 Fatty Acids
Saturated = If every carbon atom
in the chain is joined by a single
C-C bond.

Unsaturated = at least one C=C

bond.

Polyunsaturated = many double

bonds.
Most animal fats are saturated
while most plant fats are
unsaturated.
 Condensation - Esterification
Hydroxyl
Acid group
group

The link between the

glycerol molecule & each
fatty acid is an ‘Ester Link’.
6
Lipids – Phospholipids and steroids
2.1.2(h)
Keywords: phospholipid, steroid, cholesterol

Learning Objectives:

• Describe the structure of a phospholipid

• Describe how phospholipids behaviour in water
• Describe the phospholipid bilayer
• Describe the structure of cholesterol
Most phospholipids contain: Phospholipids
• a diglyceride
• a phosphate group
• a simple organic molecule such as choline
 Phospholipids - macromolecule
In phospholipids one of the fatty acids of a triglyceride is
substituted by a phosphate group.

Most of the fatty acids have an even number of carbon atoms (16
or 18), commonly one saturated and one unsaturated.
 Phospholipids in water
When in water, the
phosphate group has a
negative charge,
attracting to water,
whereas the fatty acid
tails are non-polar and
repelled by water.
 Phospholipids in water
Phospholipids may form a layer
on the surface of the water
with heads in the water and
tails sticking up out of the
water.

They may also form micelles –

tiny balls with the tails tucked
inside and the heads pointing
into the water.
 Phospholipid bilayer
Phospholipids are excellent at
forming membranes around
cells and organelles.

The phospholipids form a bilayer

with two rows of phospholipids,
tails pointing inwards and heads
pointing outwards.
 Cholesterol
• Made from 4 carbon-based rings and a hydrocarbon tail
• The ring has a polar hydroxyl (OH) group
• Fits in-between phospholipids and regulates the fluidity of
the cell surface membrane
• They bind to the hydrophobic tails causing them to pack
more closely together = more rigid.

The steroid hormones testosterone,

oestrogen and vitamin D are all made
from cholesterol.

They are hydrophobic and can pass

through the hydrophobic part of the
membrane.
 Quick quiz
1. What elements do lipids contain?
C, H, O
2. What are the components of a triglyceride?
Glycerol and 3 fatty acids
3. How are these components joined?
Esterification – a condensation reaction that forms an ester bond
4. Distinguish between saturated and unsaturated fatty acids.
Saturated fats have no double bonds, unsaturated have 1 or more
5. What component does a phospholipid contain that is absent in a
triglyceride?
Phosphate group
6. How are phospholipids arranged in the cell membrane?
In a bi-layer with their heads on the outside and tails pointing inwards.
7. Why do they arrange themselves in this way?
Their heads are polar/hydrophilic whilst their tails are
non-polar/hydrophobic.
7
Proteins – amino acids
2.1.2(k and l)
Keywords: peptide, dipeptide

Learning Objectives:

• Describe the general structure of an amino acid

• Describe the synthesis and breakdown of dipeptides and

polypeptides by the formation and breakage of peptide
bonds
 Protein
• Amino acids are monomer units,
• form a polymer called polypeptide,
• combine to form proteins.

protein
molecule

amino acid
 “Every amino acid has a central carbon atom
Draw this to which are attached four different
chemical groups”

H group
 Structure of amino acid
Basic amino acid structure - glycine Amino acid structure showing
R-groups (side chains)
The R group is different for each of the
20 amino acids
 Formation of a Peptide bond
Condensation and hydrolysis happens in the same way as in polysaccharide formation

Note that a polypeptide will have a

Peptide bond free acid group at one end and an
amino at the other.
There are a huge number of possible combinations of amino acids that can
make up proteins. A four-amino-acid structure like this has 160,000
(20x20x20x20) possible forms, because each of the amino acids in the chain
could be any one of the 20 that there are available.
8
Protein structure
2.1.2(m)
Keywords: helix, pleated, disulfide

Learning Objectives:

Describe the levels of protein structure

• - primary
• - secondary
• - tertiary
• - quaternary
 Protein – primary structure
Amino acids can be joined together to make a
polypeptide in a process called polymerisation.

“The primary structure of a protein

determines its ultimate shape and
functions”
 Protein – primary structure
Changing the amino acid can lead to change in the shape
of the protein and may stop it from functioning.

Ext. How do you think the secondary compares?

 Protein – Secondary structure
• A polypeptide has –NH+ and –C=O- groups on either side.
• These two groups form a weak hydrogen bond.
• This causes the chain to be twisted into α-Helix or beta
pleated sheet.
Protein – Secondary structure
 Protein – Tertiary structure
The α-Helix can be twisted and folded even further to
give the complex 3-D structure of each protein.
Maintained by a number of different bonds:
Disulfide bonds – Fairly strong
Ionic bonds – formed between carboxyl and amino
group, easily broken
Hydrogen bonds – numerous but easily broken.

Don’t forget to show hair example!!

 Tertiary structure
When coils and pleats start to fold, they form tertiary
structures. They are held together by:

• H-bonds =O HN-

• Ionic bonds –NH3-COO-

• Disulfide bridge --CH2S-SCH2-

 Tertiary structure
The tertiary structure of proteins
can be DENATURED by heating.

The heat increases the kinetic

energy of the molecule and makes
parts of it vibrate faster.

This means that the bonds (not

co-valent) that hold the protein in its
globular shape are broken and its
complex shape will unravel.

This is particularly important in

enzymes as it is the tertiary
structure that defines the active
site.
 Hydrophilic and hydrophobic interactions
Hydrophobic parts of the R groups
move to the centre of the
polypeptide to avoid water,
whereas hydrophilic parts move
towards the water.

These interactions cause the

twisting of the amino acid chain
which changes the shape of the
protein to form globular proteins.

This makes the protein water

soluble because water molecules
can easily cluster around them.
 Protein- Quaternary structure
• Contains a number of individual polypeptide chains
that are linked in various ways.
• There may be a non-protein
 Protein structure summary
Primary Secondary Tertiary Quaternary
structure structure structure structure
Sequence of amino Forms α-Helix or Shape formed by the Arises from a
acids found in beta pleated sheet. bending, twisting and combination of :
polypeptide chains folding of the • a number of
3-D shape due to the polypeptide helix. different
Sequence H bonds polypeptide
determines Consists of: chains
properties and • Disulfide bonds • non-protein group
functions • Ionic bond
• H bonds.

It is the 3-D structure

that controls how a
protein functions
 Quick quiz
1. What type of bond holds amino acids
together?
Peptide bond

2. What type of reaction is involved in linking

amino acids together?
Condensation reaction
3. What four different components make up an
amino acid? Amino group (-NH2)
Carboxyl group (-COOH)
Hydrogen atom (-H)
R group
9
Protein function
2.1.2(n and o)
Keywords: fibrous, globular, haemoglobin

Learning Objectives:
• Describe the properties and functions of fibrous
proteins
• Describe the structure and function of globular
proteins including a conjugated protein
 Functions of proteins

• Enzymes – Amylase
• Transport – Haemoglobin
• Movement – Actin & myosin
• Cell recognition – Antigens
• Channels – Membrane proteins
• Structure – Collagen & keratin
• Hormones – Insulin
• Protection – Antibodies
 Types of proteins
Three-dimensional tertiary and quaternary structures of
protein fall into two main categories:
Globular proteins
– Almost spherical in shape
– Soluble in water due to
position of
hydrophilic/phobic R groups
– 3D shape
– e.g. enzymes

Fibrous proteins
– Repetitive sequences of
amino acids
– Insoluble in water
– Structural
– e.g. collagen
Globular proteins
Haemoglobin -
It is made up of two α-globin and two
β-globin polypeptide chains (each
having it’s own tertiary structure).

The haem area is called a “prosthetic”

group. A molecule of oxygen can bind
to each haem group (contains iron).

Conjugated protein (has a non-protein

group attached)
 Insulin
Insulin is made of two polypeptide
chains.

The A chain begins with a section of

α-helix and the B chain ends with a
section of β-pleat.

Both chains are joined by disulfide

links.

Hydrophilic R groups are on the

outside which makes it soluble in
water.
 Amylase

Catalyses the break down of starch to maltose

A single chain of amino acids with both alpha helix and

a beta pleated sheet sections
Fibrous proteins
 Collagen

Repeating sequences of
amino acids
Each 3rd amino acid is
glycine (small R group so
can wind up tightly)
Helix shape

Made of 3 polypeptide
chains wound together like
a rope. Hydrogen bonds STRUCTURAL protein and can be
hold the chains together. found in artery walls, tendons and
bones (reinforced with calcium
phosphate).
 Keratin
Rich in cysteine so lots of
disulfide bridges between its
polypeptide chains. Alongside
hydrogen bonds, makes the
molecule very strong.

It provides mechanical
protection and also is
waterproof. It is found in
fingernails, hair, horns, scales,
fur and feathers.
 Elastin
Cross-linking and coiling make the
structure of elastin strong and
flexible.

When subjected to a stretching

force, the elastin proteins
elongate but remain attached to
each other.

Elastin can be found in our lungs,

lining blood vessels, in our
bladder and skin.
 Summary Quiz

1. The general formula for a monosaccharide is:

a) (CH2O)n
b) (CHO)n
c) C(H2O)n
d) CnH2On
 2. Sucrose is made up of:
a) glucose + fructose
b) glucose + galactose
c) glucose + glucose
d) galactose + fructose

3. Amylopectin is made up of:

a) α-1,4 glycosidic bonds
b) α-1,4 & β-1,4 glycosidic bonds
c) β-1,4 & 1,6 glycosidic bonds
d) α-1,4 & 1,6 glycosidic bonds
 4. Formation of a triglyceride does NOT involve:
a) A condensation reaction
b) Esterification
c) Polymerisation
d) A reaction between 3 fatty acids & glycerol

5. The general formula of a saturated fatty acid

is:
a) CnH2nO2
b) Cn(H2O)n
c) (CH2O)n
d) (CH2)nO
 6. Which of the following is not responsible for a
proteins tertiary structure
a) ionic bonding
b) covalent bonding
c) hydrogen bonding
d) disulphide bonding

7. Which of these is not an amino acid:

a) alanine
b) cysteine
c) glycine
d) cytosine
10
Inorganic ions
2.1.2(p)
Keywords: cation, anion

Learning Objectives:
• State the roles of key inorganic ions that are involved in
biological processes
 What is an ion?

‘Atom or molecule in which the total number of

electrons is not equal to the total number of
protons is called an ion’.
 Roles of Cations
Cations Role
Muscle contraction
Calcium ions Ca2+
Bone formation
Nerve impulse
Sodium ions Na+ Affects absorption of carbohydrate in
the intestine
Nerve impulse
Potassium ions K+
Stomatal opening
Production of ATP
Hydrogen ions H+ pH determination(more H+ ions than
OH- ions in solutions creates an acid)
Ammonium ions NH4+ Production of nitrate ions by bacteria
 Roles of Anions
Anions Role
- Component of nucleic acids
Nitrate ions NO3
A component of the nitrogen cycle
Hydrogencarbonate
Involved in the transport of CO2
ions HCO3-
- Involved in the transport of CO2
Chloride ions Cl
Regulates affinity of haemoglobin to oxygen
Component of phospholipid, ATP and nucleic
Phosphate ions
acids
PO43-
Helps root growth
Involved in regulation of blood pH(more OH-
Hydroxide ions OH- ions than H+ ions in solutions creates an
alkali)
 Quick recall
Q 1 Write the chemical symbol for the following:
a) hydrogen ion H+
b) ammonium ion NH4+
c) phosphate ion PO43-
d) hydroxide ion OH-

Q 2 Which ion is essential for the formation of bones?

Calcium ions Ca2+
Q 3 Name two ions that are important for generating nerve impulses.
Sodium ions Na+ and Potassium ions K+
Q 4 Name an ion that acts as a buffer in the blood.
Hydroxide ions OH-
Q 5 What would be the affect of adding OH- ions to a solution?
more OH- ions than H+ ions in solutions creates an alkali
 11 - 12
Qualitative tests for biological
molecules 2.1.2(q)
Keywords: Benedict’s, emulsion

Learning Objectives:

Describe how to carry out and interpret the results of the

following chemical tests:

• biuret test for proteins

• Benedict’s test for reducing and non reducing sugars
• reagent test strips for reducing sugars
• iodine test for starch
• emulsion test for lipids
 Oxidation and reduction in terms of electron transfer
Oxidation is loss of electrons. Reduction is gain of electrons (OILRIG).

The magnesium is reducing the copper(II) ions by giving them

electrons. Magnesium is a reducing agent.

The copper(II) ions are removing electrons from the magnesium to

create the magnesium ions. The copper(II) ions are acting as an
oxidising agent.
Testing for carbohydrates – PAG
9
Reducing sugars have the ability Reducing sugars – PAG 9
to give electrons to other
molecules.
Benedict’s solution contains Cu2+
ions which are reduced to Cu+
ions, forming orange-red copper
(I) oxide (Cu2O).
This is called a precipitate because
it comes out of solution and forms
a solid.
.
oxidised

reduced

deep blue red brick

 Test for reducing sugar – PAG 9

1. Add 2cm3 of food sample

(in liquid form) to a test
tube.

2. Then add 2cm3 of

Benedict’s Reagent.

3. Heat mixture for 5

minutes
The test is semi-quantitative. The original pale blue colour means
no reducing sugar, a green precipitate means little sugar; a brown
or red precipitate means more sugar is present.

Tests are important for identifying the type and

amount of sugar and can be used for diagnostic testing
in medical conditions such as diabetes.
 Reducing sugars
Observations
Sample Conclusions
0 mins After 2 mins After 4 mins
A
B
C
D
 Test for non-reducing sugars – PAG 9
Sucrose is called a non-reducing sugar since they do not have an
open chain structure.

If it is first hydrolysed (broken down) to glucose and fructose, it will

then give a positive Benedict's test.

Heat the sucrose with 2 drops of dilute hydrochloric acid for 3

minutes to hydrolyse the glycosidic bond. Cool. Neutralise the
solution by gently adding small amounts of sodium hydrogen
carbonate powder.

Test as before for reducing sugars.

 Non-Reducing sugars
Observations
Sample Conclusions
0 mins After 2 mins After 4 mins
A
B
C
D
 Test for starch – PAG 9
1. Add iodide
solution to
sample.

2. If starch is present,
it will change from
yellow-brown to
blue-black.

When dissolved in potassium

iodide, the iodide forms a
triiodide ion which slips into the
middle of the amylose helix and
causes a colour change.
Testing for lipids – PAG 9
 The Emulsion test determines the presence lipids.

Soild sample : Liquid sample:

Crush the food sample and place Add a few drops of the liquid
in a dry test tube. food sample to a dry test tube.

Add ethanol to the sample and Add 2 cm3 ethanol and shake it
shake thoroughly. thoroughly

Allow the solid to settle (about 3 Add 2 cm3 of water.

min) to allow the lipid to be
extracted.

Decant the ethanol into another

test tube.

Add 2 cm3 of water to the second

test tube.
 Results and Interpretation
observation interpretation

Positive test A layer of cloudy white suspension Lipids are present

forms in the solution. (tiny globules
of fat suspended in the solution can
be seen. This is an emulsion. Foods
with high lipid content have a
‘higher’ layer than foods with less).

Negative Solution remains colourless. No Lipids are not present

test emulsion is formed.
 Principle of the Ethanol Emulsion Test
Lipids are non-polar organic compounds and are soluble in organic
solvents such as ethanol (alcohol), but insoluble in water. Ethanol
is miscible in water.

As ethanol is miscible with lipids no change is seen upon its

addition. When water is added the lipids are dispersed as micelles
(small droplets) throughout the solution of ethanol and water.

A layer is formed at the top as lipids are less dense than water.
State some precautions taken during the emulsion
test
To avoid contamination:

a. Clean apparatus should be used

b. Hands were washed between testing different food

samples and

c. Food samples were kept separate from each other.

Testing for proteins – PAG 9
 Test for protein – PAG 9
If protein is
present, the
colour changes
from light blue to
lilac.

The colour is formed by a

complex between nitrogen
atoms in peptide bond and
Cu2+ ions.
 13-14
Quantitative tests for biological
molecules 2.1.2(r)
Keywords: colorimeter, supernatant

Learning Objectives:
Describe quantitative methods to determine the
concentration of a chemical substance in a solution to
include:
• - colorimetry
• - use of biosensors
 Using a colorimeter – PAG 5
1. Place supernatant in cuvette.
2. Add red filter:

- if the supernatant is blue,

absorption of red is high and % of
A colorimeter works by
transmission is low (lots of
measuring the amount of light
unreacted copper sulfate).
that passes through a sample.
- if the supernatant is less blue,
absorption of red light is low and %
of transmission is high (little
unreacted copper sulfate).
3. In-between readings, zero with a
‘blank’ sample of water.
 Calibration curve for known concentrations of glucose
– PAG 5
1. Take known concentrations
of reducing sugars.

2. Use a colorimeter to record

the percentage transmission
of light through each
supernatant.

3. Plot a graph of ‘transmission

of light’ against the
concentration of reducing
sugar. This provides a For example, using the
calibration curve which can calibration curve, if a sample
be used to determine the had a transmission of 92%, it
concentration of unknown contains 12gdm-3 of glucose.
samples.
 Use of biosensors – PAG 5
Biosensors work by taking
a biological or chemical
variable (analyte – e.g.
glucose) which cannot be
easily measured which is
then converted into an
electrical signal.

The biological component (often immobilised), recognises and

interacts with the analyte to produce a physical change (a signal)
that can be detected, by the transducer.
15 -16
Chromatography
2.1.2(s)
Keywords: solvent, chromatogram

Learning Objectives:

• Describe the principles and uses of paper and thin layer

chromatography to separate biological molecules/compounds

• Interpret practical investigations to analyse biological

solutions using paper and thin layer chromatography
 Using thin layer chromatography (TLC) to
separate photosynthetic pigments - PAG 6
Thin-layer chromatography (TLC) is a technique used to separate
pigments using a thin layer of adsorbent material, known as the
stationary phase.

After the sample has been applied on the material, a solvent (known as
the mobile phase) moves up the material. Because different pigments
move up the TLC plate at different rates, separation is achieved.

After the experiment, the spots are visualised.

The distance travelled by the pigment is divided by the total distance

travelled by the solvent. This ratio is called the retention factor or Rf. In
general, a pigment which moves very little, will have low Rf, while one
that moves further, will have high retention factor.
 Calculating Rf values
• Scientists use a measurement
called Rf to help distinguish
different pigments on a
chromatogram.

• To calculate the Rf values for a

pigment use this formula:
Rf = a ÷ b

• a is the distance (in cm) moved

by the pigment

• b is the distance moved (in cm)

by the solvent.
 Worked example

3.1
Rf =
4.8

4.8cm
3.1cm
= 0.65

1. Calculate the Rf values

Rf values for the main amino acids
Amino acid Rf value
Lysine 0.14
Arginine 0.20
Aspartic acid 0.24
Glycine 0.26
Serine 0.27
Glutamic acid 0.30
Threonine 0.35
Alanine 0.38
Proline 0.43
Tyrosine 0.45
Methionine 0.55
Valine 0.60
Phenylalanine 0.68
Isoleucine 0.72
Leucine 0.73
 Difficulties…
Sometimes with colourless
molecules, you cannot se where
they finish. To overcome this:

- ultraviolet light can be used.

Plates fluoresce under UV light
except where the spots have
travelled.

- Ninhydrin binds to amino acids

which makes them visible.

- iodine gas binds to molecules

in each spot.
 How does it work?
The height moved by the
molecules depends on their
solubility and polarity.

Exposed –OH groups of the

paper allow hydrogen bonds
with the molecules.

A highly polar solute will stick

to the surface and move
slowly. A non-polar solute
will travel very quickly up the
plate.
 MCQs for 2.1.2
Biochem 1 = turquoise
Biochem 2 = pink

Write two sets of 1-20 and go round the room

answering the questions.