AS 2 Biological Molecules

Metabolism
total sum of all the biochemical reactions in the body

Macromolecule
a large molecule such as polysaccharide, protein or nucleic acid
are described as polymers
made up of monomers

Monomers
relatively simple molecule which is used as a basic building block for the synthesis
of a polymer
many monomers are joined together by covalent bonds to make the polymer by
condensation reaction

Polymer
giant molecule made from many similar repeating subunits joined together in a
chain
the subunits are monomers (smaller and simpler)

Condensation Reaction
the joining together of 2 monomers by the removal of a water molecule
 Adding water to split a molecule is called hydrolysis

The key biological molecules

Carbohydrates
Carbohydrates are one of the main carbon-based compounds in living organisms
All molecules in this group contain C, H and O
H and O atoms are always present in the ratio of 2:1
3 Types
The Two Forms of Glucose
alpha (α) glucose
beta (β) glucose

Uses
source of energy
building blocks for larger molecules

Starch & Glycogen

 are polysaccharides
These chains may be:
Branched or unbranched
Folded (making the molecule compact which is ideal for storage eg. starch and
glycogen)
Straight (making the molecules suitable to construct cellular structures
e.g.cellulose) or coiled
Starch and glycogen are storage polysaccharides because they are:
Compact (so large quantities can be stored)
Insoluble (so will have no osmotic effect, unlike glucose which would lower the
water potential of a cell causing water to move into cells, cells would then
have to have thicker cell walls - plants or burst if they were animal cells)

Starch
storage polysaccharide of plants
Due to the many monomers in a starch molecule, it takes longer to digest than
glucose
constructed from two different polysaccharides:
Amylose (10 - 30% of starch)
Unbranched helix-shaped chain with 1,4 glycosidic bonds between α-
glucose molecules
 made by condensations between alpha glucose molecules

Amylopectin (70 - 90% of starch)

 1,4 glycosidic bonds between α-glucose molecules but also 1,6 glycosidic
bonds form between glucose molecules creating a branched molecule

Glycogen
storage polysaccharide of animals and fungi
highly branched and not coiled
highest concentration in liver and muscles due to cellular respiration
more branched than amylopectin making it more compact which helps animals
store more
Cellulose
polysaccharide
These chains may be:
Branched or unbranched
Folded (making the molecule compact which is ideal for storage, eg. starch
and glycogen)
Straight (making the molecules suitable to construct cellular structures, eg.
cellulose) or coiled
Polysaccharides are insoluble in water
long chains of β-glucose joined together by 1,4 glycosidic bonds
 β-glucose molecules must be rotated 180° to each other

many hydrogen bonds form between the long chains giving cellulose itʼs strength
Function
main structural component of cell walls
The high tensile strength of cellulose allows it to be stretched without
breaking which makes it possible for cell walls to withstand turgor pressure
The strengthened cell walls provides support to the plant

Dipole & Hydrogen Bond

Each shared pair of electron form a covalent bond

Dipole
The unequal distribution of charge
Hydrogen Bond
the negatively charged oxygen of one molecule is attracted to a positive charged
hydrogen of another

Polar molecules
are attracted to water molecules because the water molecules also have dipoles
such molecules are hydrophilic ( water loving) and tend to be soluble in water

Lipids
Macromolecules which contain carbon, hydrogen and oxygen atoms. However,
unlike carbohydrates lipids contain a lower proportion of oxygen
Non-polar and hydrophobic
Different types:
Fats and Oils (composed mainly of triglycerides)
Phospholipids
Steroids and waxes

Fatty Acids
Fatty acids can vary in two ways:
Length of the hydrocarbon chain
The fatty acid may be saturated (mainly in animal fat) or unsaturated
C=C are unsaturated
Double bond make fatty acid & lipids melt more easily

Triglycerides
3 fatty acids combine with 1 glycerol to form a triglyceride
Are non-polar, hydrophobic molecules
most common lipids
The monomers are glycerol and fatty acids
 Glycerol is an alcohol (an organic molecule that contains a hydroxyl group
bonded to a carbon atom)

Function
energy storage because they are rich in C-H bonds (higher calorific value)
insulator against loss of heat
increase ability to float more easily
protects organs from risk of damage

Phospholipids
special type of lipid
only two fatty acids bonded to a glycerol
polar so soluble in water
hydrophilic polar head
hydrophobic tails

amphipathic (they have both hydrophobic and hydrophilic parts)

Role
main component of cell membranes
hydrophilic phosphate heads form H-bonds with water
This enables the cells to organise specific roles into organelles helping
with efficiency
contributes to the fluidity of the cell membrane
mainly unsaturated fatty acid tails then the membrane will be more fluid
control membrane protein orientation
 Weak hydrophobic interactions between the phospholipids and
membrane proteins hold the proteins within the membrane but still allow
movement within the layer

Proteins
polymers made up of amino acids
Uses
all enzymes are proteins
essential component of cell membrane
hormones
antibodies are proteins
college is a protein
maybe storage products

Amino Acids
monomers of proteins
20 amino acids found in proteins
general structure of all amino acids is a central carbon atom bonded to:
An amine group -NH
A carboxylic acid group -COOH
A hydrogen atom
 An R group

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

Structure of Protein
There are four levels of structure in proteins
Primary
The sequence of amino acids bonded by covalent peptide bonds
The primary structure is specific for each protein
Secondary
occurs when the weak negatively charged nitrogen and oxygen atoms interact
with the weak positively charged hydrogen atoms to form hydrogen bonds
There are two shapes that can form due to hydrogen bonds:
α-helix
β-pleated sheet
The α-helix shape occurs when the hydrogen bonds form between every
fourth peptide bond (between the oxygen of the carboxyl group and the
hydrogen of the amine group)
The β-pleated sheet shape forms when the protein folds so that two parts of
the polypeptide chain are parallel to each other enabling hydrogen bonds to
form between parallel peptide bonds
Most fibrous proteins have secondary structures
The secondary structure only relates to hydrogen bonds forming between the
amino group and the carboxyl group
 The hydrogen bonds can be broken by high temperatures and pH changes

Tertiary
Further conformational change of the secondary structure leads to additional
bonds forming between the R groups
The additional bonds are:
Hydrogen (these are between R groups)
Disulphide (only occurs between cysteine amino acids)
Ionic (occurs between charged R groups)
Weak hydrophobic interactions (between non-polar R groups)
 This structure is common in globular proteins

Quaternary
Occurs in proteins that have more than one polypeptide chain working
together as a functional macromolecule, for example, haemoglobin
Each polypeptide chain in the quaternary structure is referred to as a subunit
of the protein
Proteins: Interactions & Shape
A polypeptide chain will fold differently due to the interactions (and hence the
bonds that form) between R groups
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
Ionic
 Globular Fibrous

compact, roughly circular form long strands

soluble in soluble

non-polar hydrophobic R groups are

orientated towards and their polar
hydrophilic R groups orientate
themselves on the outside of the protein

Some globular proteins are conjugated

proteins that contain a prosthetic group
Haemoglobin
globular protein
made up of 4 polypeptide chains
subunits are:
two α–globins
two β–globins
shape is nearly spherical
The four globin subunits are held together by disulphide bonds and arranged so
that their hydrophobic R groups are facing inwards and the hydrophilic R groups
are facing outwards
this helps to maintain 3 dimensional shape and its solubility
 Function
responsible for binding oxygen in the lung and transporting the oxygen to
tissue to be used in aerobic metabolic pathways
As oxygen is not very soluble in water and haemoglobin is, oxygen can be
carried more efficiently around the body when bound to the haemoglobin
The presence of the haem group (and Fe ) enables small molecules like oxygen
to be bound more easily because as each oxygen molecule binds it alters the
quaternary structure
The existence of the iron II ion (Fe ) in the prosthetic haem group also allows
oxygen to reversibly bind as none of the amino acids that make up the
polypeptide chains in haemoglobin are well suited to binding with oxygen

Collagen
 most common proteins in animals
insoluble fibrous protein
structural protein
connective tissue

Structure
formed from three polypeptide chains closely held together by hydrogen bonds to
form a triple helix
Each polypeptide chain is a helix shape 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
crosslinks hold the collagen molecules together to form fibrils
The collagen molecules are positioned in the fibrils so that there are staggered
ends
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

Function
Flexible structural protein forming connective tissues
The presence of the many hydrogen bonds within the triple helix structure of
collagen results in great tensile strength.
The staggered ends of the collagen molecules within the fibrils provide
strength
 Collagen is a stable protein due to the high proportion of proline and
hydroxyproline amino acids result in more stability as their R groups repel
each other
Length of collagen molecules means they take too long to dissolve in water

Water Molecules:
Water is composed of atoms of hydrogen and oxygen. One atom of oxygen
combines with two atoms of hydrogen by sharing electrons
Although water as a whole is electrically neutral the sharing of the electrons is
uneven between the oxygen and hydrogen atoms
The oxygen atom attracts the electrons more strongly than the hydrogen
atoms, resulting in a weak negatively charged region on the oxygen atom (δ )
and a weak positively charged region on the hydrogen atoms(δ ), this also
results in the asymmetrical shape
Water is a polar molecule

Hydrogen bonds form between water molecules

As a result of the polarity of water hydrogen bonds form between the positive
and negatively charged regions of adjacent water molecules
Hydrogen bonds are weak, when there are few, so they are constantly breaking
and reforming. However when there are large numbers present they form a strong
structure
Hydrogen bonds contribute to the many properties water molecules have that
make them so important to living organisms:
An excellent solvent – many substances can dissolve in water
A relatively high specific heat capacity
A relatively high latent heat of vaporisation
Water is less dense when a solid
Water has high surface tension and cohesion
 It acts as a reagent

Solvent
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)

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.
The high specific heat capacity is due to the many hydrogen bonds present in
water.
The advantage for living organisms is that it:
Provides suitable habitats
 Allows for constant temperatures within bodies and cells to be maintained

Latent heat of vaporisation

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 provides a cooling effect for living organisms, for example the transpiration
from leaves or evaporation of water in sweat on the skin