THE CHEMISTRY FOR BIOLOGISTS

THE CHEMISTRY OF LIFE

CARBOHYDRATE
LIPIDS
PROTEINS
 LEARNING OBJECTIVES
Understand the importance of water as a solvent in
transport, including it's dipole nature.
 Biology is the study of living
things, but living things consist of
chemical substances.
Ionic Bonding
the atoms involved in the
reaction give or receive electrons.
Covalent Bonding
the atoms involved in the reaction share electrons
The Importance of Inorganic ions
when ionic substances dissolve in water, the ions separate in process --> dissociation

contains 60 - 70%

most ionic
substances exist
as positive and
negatife ions
 The importance of inorganic ions

1. sodium ions 1. nitrate ions

2. calcium ions 2. phosphate ions
3. hydrogen ions 3. chloride ions
4. magnesium ions 4. hydrogencarbonate ions
THE CHEMISTRY OF WATER

all the reactions in living cells take

place in water.

water is major habitat and support

other parts of the planet

water is polar molecules

 this polarity --> HYDROGEN BONDS

hydrogen bond is weak but there are many of

them so molecules of water 'stick together'. The covalent bonds of water make it a polar molecule
 the importance of water
1. water as polar solvent.
most of chemical reactions within cell occur in water.
As water is a polar molecule many ions (e.g. sodium chloride) and covalently bonded polar substances (e.g.
glucose) will dissolve in it
This allows chemical reactions to occur within cells (as the dissolved solutes are more chemically reactive
when they are free to move about)
Metabolites can be transported efficiently (except non-polar molecules which are hydrophobic)

2. water as transport medium.

because the dipole nature of water, enables many different substances to
dissolve in it.
 the importance of water
3. A relatively high specific heat capacity
The specific heat capacity of a substance is the amount of thermal energy required to raise the temperature of 1kg of that substance
by 1°C. Water’s specific heat capacity is 4200 J/kg°C
The high specific heat capacity is due to the many hydrogen bonds present in water. It takes a lot of thermal energy to break these
bonds and a lot of energy to build them, thus the temperature of water does not fluctuate greatly
The advantage for living organisms is that it:
Provides suitable habitats
Allows for constant temperatures within bodies and cells to be maintained (this ensures enzymes have the optimal
temperatures)
This is because a large increase in energy is needed to increase the temperature of water

4. A relatively high latent heat of vaporization

In order to change state (from liquid to gas) a large amount of thermal energy must be absorbed by water to break
the hydrogen bonds and evaporate
This is an advantage for living organisms as only a little water is required to evaporate for the organism to lose a
great amount of heat
This provides a cooling effect for living organisms, for example the transpiration from leaves or evaporation of water
in sweat on the skin
 the importance of water

5. Water is less dense when a solid

it can not be compressed.
its become important factor in many hydraulic mechanisms in living organism.

6. Water has high surface tension and cohesion

they are attracted to other different molecules makes water become adhesive.
water has very high surface tension because the attraction between water molecules, including hydrogen
bonds is greater than the attraction between water molecules and the air.
The key biological molecules for living organisms
Biological molecules are
the key to structure
and function of living
things.
CARBOHYDRATE
 LEARNING OBJECTIVES
Know the difference between monosaccharides, disaccharides and
polysaccharides, including glycogen and starch (amylose and amylopectin)
be able to relate the structures of monosaccharides, disaccharides and
polysaccharides to their roles in providing and storing energy
know how monosaccharides (glucose, fructose and galactose) join together
to form disaccharides (maltose, sucrose and lactose) and polysaccharides
(glycogen, amylose and amylopectin) through condensation reactions
forming glycosidic bonds, and how these can be split through hydrolysis
reactions
 Biological
molecules

N
organic compounds
contains of
C H O
s

P
 each carbon atom can
make 4 bonds, and so it
can connect to four other
atoms.
CARBOHYDRATE 3 main groups
as energy sources
MONOSACCHARIDES
storing energy

DISACCHARIDES
part of cell wall in plants,

fungi, bacteria POLYSACCHARIDE

 Carbohydrates
Carbohydrates are one of the main carbon-based compounds in living organisms
All molecules in this group contain C, H and O
As H and O atoms are always present in the ratio of 2:1 (eg. water H2O, which is where
‘hydrate’ comes from) they can be represented by the formula Cx (H2O)y
The three types of carbohydrates are monosaccharides, disaccharides and
polysaccharides
MONOSACCHARIDES
simple sugar with one atom oxygen and two hydrogen atoms for each carbon atom in the
molecule.

general formulae : (CH2O)n

Triose sugars (n=3) Pentose sugars (n=5) Hexose sugars (n=6)

three carbons
five carbons six carbons
C3H6O3
C5H10O5 C6H12O6
found in mitochondria
ex: DNA - RNA ex: glucose, galactose and
fructose.
 Find the difference
between alpha and beta Glucose.
DISACCHARIDES
consist of two monossacharides joined together.
 POLYSACCHARIDES
made of many monosaccharides units joined by condensation
reactions that create glycosidic bond.

the glycosidic bond can be spilt by hydrolysis.

hydrolysis takes place during digestion in the gut, in the muscle and
liver cells (during the cellular respiration).
 Condensation
Also known as dehydration synthesis (‘to put together while losing water’)
A condensation reaction occurs when monomers combine together by covalent
bonds to form polymers (polymerization) or macromolecules (lipids) and water is
removed
 Hydrolisis
Hydrolysis means ‘lyse’ (to break) and ‘hydro’ (with water)
In the hydrolysis of polymers, covalent bonds are broken when water is added
CARBOHYDRATE AND ENERGY
 any glucose in the food you eat can be used and
absorbed directly in your cells.
It's good source of relatively instant energy.

But why these food can't be used to store energy?

 ideals as energy storage :
1. form very compact molecules, which take up
space.
2. physically and chemically inactive, they do
not interfere other functions of the cell.
3. not very soluble in water, no effect on water
potential and water movements (osmosis)

POLYSACCHARIDES

STARCH GLYCOGEN
 energy store in plants
the sugars produce during Photosynthesis, and rapidly converted into starch
(insoluble).
this starch can be broken down to release glucose when it's needed.
Starch consists of long chains -glucose.

AMYLOSE : unbranched polymer of between 200 - 5000 glucose units.

AMYLOPECTIN : a branched polymer of glucose units.

STARCH
 AMYLASE
has only 1,4 glycosidic bond

AMYLOPECTIN
has 1,4 glycosidic bond and 1,6
glycosidic bond

this combination become

STARCH
 GLYCOGEN
known as animal starch
sometimes found in fungi.
glycogen has more 1,6 glycosidic bond rather than amylopectin.
this causes glycogen can be break down rapidly.
The branching enables more free ends where glucose molecules can either be added or
removed allowing for condensation and hydrolysis reactions to occur more rapidly – thus the
storage or release of glucose can suit the demands of the cell
explain how the structure of
carbohydrates is related to
their function as storage
molecules providing the fuel
for cellular respiration?
LIPID
 LEARNING OBJECTIVES
know how a triglyceride is synthesised by the formation of ester
bonds during condensation reactions between glycerol and three
fatty acids
know the differences between saturated and unsaturated lipids
TRIGLYCERIDE
Macromolecules which contain carbon, hydrogen and oxygen atoms. However,
unlike carbohydrates lipids contain a lower proportion of oxygen
Non-polar and hydrophobic (insoluble in water)
Different types:
Fats and Oils (composed mainly of Triglycerides)
Phospholipids
Steroids and waxes (considered lipids as they are hydrophobic thus
insoluble in water)
1. TRIGLYCERIDE
 Are non-polar, hydrophobic molecules
The monomers are glycerol and fatty acids
Glycerol is an alcohol (an organic molecule that contains a hydroxyl group bonded to a
carbon atom)
Fatty acids contain a methyl group at one end of a hydrocarbon chain (chains of
hydrogens bonded to carbon atoms, typically 4 to 24 carbons long) and at the other is a
carboxyl group
Fatty acids can vary in two ways:
1. Length of the hydrocarbon chain
2. The fatty acid may be saturated (mainly in animal fat) or unsaturated (mainly
vegetable oils, although there are exceptions e.g. coconut and palm oil)
Unsaturated fatty acids can be mono
or poly-unsaturated

If H atoms are on the same side of the

double bond they are cis-fatty acids
and are metabolised by enzymes
If H atoms are on opposite sides of the
double bond they are trans-fatty acids
and cannot form enzyme-substrate
complexes, therefore, are not
metabolised. They are linked with
coronary heart disease
 Saturated and Unsaturated Fatty Acid
each carbon atom is joined
to the one next to it by
single covalent bond.

has one carbon-carbon

double bond

has more than one carbon-

carbon double bond
 Triglycerides: Structure & Function
1. Energy storage
The long hydrocarbon chains contain many carbon-hydrogen bonds with little oxygen
(triglycerides are highly reduced)
So when triglycerides are oxidised during cellular respiration this causes these
bonds to break releasing energy used to produce ATP
Triglycerides therefore store more energy per gram than carbohydrates and proteins
(37kJ compared to 17kJ)
As triglycerides are hydrophobic they do not cause osmotic water uptake in cells so
more can be stored
Plants store triglycerides, in the form of oils, in their seeds and fruits. If extracted
from seeds and fruits these are generally liquid at room temperature due to the
presence of double bonds which add kinks to the fatty acid chains altering their
properties
Mammals store triglycerides as oil droplets in adipose tissue to help them survive
when food is scarce (e.g. hibernating bears)
 Triglycerides: Structure & Function
1. Energy storage

The oxidation of the carbon-hydrogen bonds releases large numbers of water molecules
(metabolic water) during cellular respiration
Desert animals retain this water if there is no liquid water to drink
Bird and reptile embryos in their shells also use this water
 Triglycerides: Structure & Function
2. Insulation
Triglycerides are part of the composition of the myelin sheath that surrounds
nerve fibres
This provides insulation which increases the speed of transmission of nerve
impulses
Triglycerides compose part of the adipose tissue layer below the skin which acts
as insulation against heat loss (eg. blubber of whales)

3. Buoyancy
The low density of fat tissue increases the ability of animals to float more easily

4. Protection
The adipose tissue in mammals contains stored triglycerides and this tissue helps
protect organs from the risk of damage
 Forming Ester Bond
Triglycerides are formed by esterification
An ester bond forms when the hydroxyl (-OH)
group of the glycerol bonds with the carboxyl
group (-COOH) of the fatty acid
The formation of an ester bond is a
condensation reaction
For each ester bond formed a water
molecule is released
Three fatty acids join to one glycerol
molecule to form a triglyceride
Therefore for one triglyceride to form,
three water molecules are released
 2.phospholipid
Phospholipids are a type of lipid, therefore
they are formed from the monomers glycerol
and fatty acids
Unlike triglycerides, there are only two fatty
acids bonded to a glycerol molecule in a
phospholipid as one has been replaced
by a phosphate ion (PO43-)
As the phosphate is polar it is soluble in water
(hydrophilic)
The fatty acid ‘tails’ are non-polar and
therefore insoluble in water (hydrophobic)
Phospholipids are the major components of cell surface membranes. They
have fatty acid tails that are hydrophobic and a phosphate head, that is
hydrophilic, attached to a glycerol molecule.

Phospholipids are amphipathic (they have both hydrophobic and hydrophilic

parts)
As a result of having hydrophobic and hydrophilic parts, phospholipid molecules
form monolayers or bilayers in water
Phospholipids vs Triglycerides Table
 3. Steroid (Cholesterol)
Just like phospholipid molecules, cholesterol molecules have hydrophobic and hydrophilic
regions
Their chemical structure allows them to exist in the bilayer of the membrane
Molecules of cholesterol are synthesised in the liver and transported via the blood
Cholesterol affects the fluidity and permeability of the cell membrane
It disrupts the close-packing of phospholipids, increasing the flexibility of the
membrane
It acts as a barrier, fitting in the spaces between phospholipids. This prevents water-
soluble substances from diffusing across the membrane
Molecules of cholesterol are used to produce steroid-based hormones such as oestrogen,
testosterone and progesterone
The structure of a cholesterol molecule possesses both a
hydrophobic region and a hydrophilic region
Biochemical Tests: Lipids
Lipids are nonpolar molecules
that do not dissolve in water but
will dissolve in organic
solvents such as ethanol

Results
If lipids are present, a milky
emulsion will form (the solution
appears ‘cloudy’); the more lipid
present, the more obvious the
milky colour of the solution
If no lipid is present, the solution
remains clear
PROTEIN
 LEARNING OBJECTIVES
Know the basic structure of an amino acid.
Understand the formation of polypeptides and proteins, as amino acid
monomers linked together by condensation reactions to form peptide
bonds.
Understand the significance of a protein’s primary structure in determining its
secondary structure, three-dimensional structure and properties, and the
types of bond involved in its three-dimensional structure.
Know the molecular structure of a globular protein and a fibrous protein
and understand how their properties relate to their functions (including
haemoglobin and collagen).
 PROTEIN
Proteins are polymers (and macromolecules) made of monomers called amino acids
Protein contains of Hydrogen, Carbon, Oxygen and some of N,S or P.

Proteins are extremely important in cells because they form all of the following:
Enzymes
Cell membrane proteins (eg. carrier)
Hormones
Immunoproteins (eg. immunoglobulins)
Transport proteins (eg. haemoglobin)
Structural proteins (eg. keratin, collagen)
Contractile proteins (eg. myosin)
The general structure of all amino acids is a central carbon atom bonded to:
An amino group -NH2
A carboxylic acid group -COOH
A hydrogen atom
An R group (which is how each amino acid differs and why amino acid
properties differ e.g. whether they are acidic or basic or whether they are polar
or non-polar)
1
Bond in Protein
Peptide Bond
3 Hydrogen Bond
Disulfide Bond
Ionic Bond
2
 PEPTIDE BONDS

Amino acids are bonded together by covalent peptide bonds

to form a dipeptide in a condensation reaction
 Forming Peptide Bond
In order to form a peptide bond a hydroxyl (-OH) is lost from a carboxylic group
of one amino acid and a hydrogen atom is lost from an amine group of another
amino acid
The remaining carbon atom (with the double-bonded oxygen) from the first
amino acid bonds to the nitrogen atom of the second amino acid
This is a condensation reaction so water is released. The resulting molecule is a
dipeptide
When many amino acids are bonded together by peptide bonds the molecule
formed is called a polypeptide. A protein may have only one polypeptide chain
or it may have multiple chains interacting with each other
During hydrolysis reactions polypeptides are broken down to amino acids
when the addition of water breaks the peptide bonds
PROTEIN STRUCTURE
PRIMARY STRUCTURE
SECONDARY STRUCTURE
TERTIARY STRUCTURE
QUARTERNARY STRUCTURE
differences between
protein structure
A polypeptide chain will fold differently
due to the interactions (and hence the
bonds that form) between R groups. The
three-dimensional configuration that
forms is called the tertiary structure of a
protein
Each of the twenty amino acids that make
up proteins has a unique R group and
therefore many different interactions can
occur creating a vast range of protein
configurations and therefore functions
Within tertiary structured proteins are the
following bonds:
Strong covalent disulphide
Weak hydrophobic interactions
Weak hydrogen Proteins:
Ionic

Interactions & Shape

Globular proteins are compact, roughly spherical (circular) in shape and soluble in water
Globular proteins form a spherical shape when folding into their tertiary structure because:
their non-polar hydrophobic R groups are orientated towards the centre of the protein
away from the aqueous surroundings and
their polar hydrophilic R groups orientate themselves on the outside of the protein
This orientation enables globular proteins to be (generally) soluble in water as the water

Globular
molecules can surround the polar hydrophilic R groups
The solubility of globular proteins in water means they play important
physiological roles as they can be easily transported around organisms and be
involved in metabolic reactions
The folding of the protein due to the interactions between the R groups results in globular
proteins having specific shapes. This also enables globular proteins to play physiological
roles, for example, enzymes can catalyse specific reactions and immunoglobulins can
respond to specific antigens
Some globular proteins are conjugated proteins that contain a prosthetic group eg.
haemoglobin which contains the prosthetic group called haem
Haemoglobin
Haemoglobin is a globular protein which is an oxygen-carrying pigment found in vast quantities in
red blood cells
It has a quaternary structure as there are four polypeptide chains. These chains or subunits are
globin proteins (two α–globins and two β–globins) and each subunit has a prosthetic haem group
The four globin subunits are held together by disulphide bonds and arranged so that their
hydrophobic R groups are facing inwards (helping preserve the three-dimensional spherical shape)
and the hydrophilic R groups are facing outwards (helping maintain its solubility)
The arrangements of the R groups is important to the functioning of haemoglobin. If changes occur
to the sequence of amino acids in the subunits this can result in the properties of haemoglobin
changing. This is what happens to cause sickle cell anaemia (where base substitution results in the
amino acid valine (non-polar) replacing glutamic acid (polar) making haemoglobin less soluble)
The prosthetic haem group contains an iron II ion (Fe2+) which is able to reversibly combine with an
oxygen molecule forming oxyhaemoglobin and results in the haemoglobin appearing bright red
Each haemoglobin with the four haem groups can therefore carry four oxygen molecules (eight
oxygen atoms)
Fibrous proteins are long strands of polypeptide chains
that have cross-linkages due to hydrogen bonds
They have little or no tertiary structure
Due to the large number of hydrophobic R groups
fibrous proteins are insoluble in water
Fibrous proteins have a limited number of amino acids
with the sequence usually being highly repetitive

structures that are strong and this along with their

insolubility property, makes fibrous proteins very
Fibrous
The highly repetitive sequence creates very organised

suitable for structural roles, for example, keratin that

makes up hair, nails, horns and feathers and collagen
which is a connective tissue found in skin, tendons and
ligaments
Collagen
Collagen is formed from three polypeptide chains closely held together by hydrogen bonds to
form a triple helix (known as tropocollagen)
Each polypeptide chain is a helix shape (but not α-helix as the chain is not as tightly wound) and
contains about 1000 amino acids with glycine, proline and hydroxyproline being the most common
In the primary structure of collagen almost every third amino acid is glycine
This is the smallest amino acid with a R group that contains a single hydrogen atom
Glycine tends to be found on the inside of the polypeptide chains allowing the three chains to be
arranged closely together forming a tight triple helix structure
Along with hydrogen bonds forming between the three chains there are also covalent bonds present
Covalent bonds also form cross-links between R groups of amino acids in interacting triple helices
when they are arranged parallel to each other. The cross-links hold the collagen molecules together
to form fibrils
The collagen molecules are positioned in the fibrils so that there are staggered ends (this gives the
striated effect seen in electron micrographs)
When many fibrils are arranged together they form collagen fibres
Collagen fibres are positioned so that they are lined up with the forces they are withstanding
 Differences
Collagen and Haemoglobin
CONJUGATED PROTEINS
some proteins molecules are joined
with (conjugated to) another molecule
called a prosthetic group.
 Covalent bonds in
organic molecules
table