Contents

Water
Carbohydrates
Lipids
Proteins

BIOLOGICAL MOLECULES

At least 80% of the mass of living organisms is water, and

almost all the chemical reactions of life take place in aqueous
solution. The other chemicals that make up living things are
mostly organic macromolecules belonging to the 4 groups
proteins, nucleic acids, carbohydrates or lipids. These
macromolecules are made up from specific monomers as shown
in the table below. Between them these four groups make up
93% of the dry mass of living organisms, the remaining 7%
comprising small organic molecules (like vitamins) and inorganic
ions.
GROUP NAME MONOMERS POLYMERS % DRY MASS
Proteins amino acids polypeptides 50
nucleic acids nucleotides polynucleotides 18
carbohydrates monosaccharides polysaccharides 15

GROUP NAME COMPONENTS LARGEST UNIT % DRY MASS

lipids fatty acids + glycerol Triglycerides 10
The first part of this unit is about each of these groups. We'll
look at each of these groups in detail, except nucleic acids,
which are studied in module 2.

WATER

Water molecules are charged, with the oxygen atom being

slightly negative and the hydrogen atoms being slightly positive.
These opposite charges attract each other, forming hydrogen
bonds. These are weak, long distance bonds that are very
common and very important in biology.
Water has a number of important properties essential for life.
Many of the properties below are due to the hydrogen bonds in
water.

• Solvent. Because it is charged, water is a very good

solvent. Charged or polar molecules such as salts, sugars
and amino acids dissolve readily in water and so are
called hydrophilic ("water loving"). Uncharged or non-
polar molecules such as lipids do not dissolve so well in
water and are called hydrophobic ("water hating").
• Specific heat capacity. Water has a specific heat
capacity of 4.2 J g-1 °C-1, which means that it takes 4.2
joules of energy to heat 1 g of water by 1°C. This is
unusually high and it means that water does not change
temperature very easily. This minimizes fluctuations in
temperature inside cells, and it also means that sea
temperature is remarkably constant.
• Latent heat of evaporation. Water requires a lot of
energy to change state from a liquid into a gas, and this
is made use of as a cooling mechanism in animals
(sweating and panting) and plants (transpiration). As
water evaporates it extracts heat from around it, cooling
the organism.
• Density. Water is unique in that the solid state (ice) is
less dense that the liquid state, so ice floats on water. As
the air temperature cools, bodies of water freeze from
the surface, forming a layer of ice with liquid water
underneath. This allows aquatic ecosystems to exist even
in subzero temperatures.
• Cohesion. Water molecules "stick together" due to their
hydrogen bonds, so water has high cohesion. This
explains why long columns of water can be sucked up tall
trees by transpiration without breaking. It also explains
surface tension, which allows small animals to walk on
water.
• Ionization. When many salts dissolve in water they
ionize into discrete positive and negative ions
(e.g. NaCl Na+ + Cl-). Many important biological
molecules are weak acids, which also ionize in solution
(e.g. acetic acid acetate- + H+). The names of the acid
and ionized forms (acetic acid and acetate in this
 example) are often used loosely and interchangeably,
which can cause confusion.
You will come across many examples of two names referring to
the same substance, e.g.:
phosphoric acid and phosphate, lactic acid and lactate,
citric acid and citrate, pyruvic acid and pyruvate, aspartic
acid and aspartate, etc. The ionized form is the one found
in living cells.
• pH. Water itself is partly ionized (H2O H+ + OH- ), so it is a
source of protons (H+ ions), and indeed many biochemical
reactions are sensitive to pH (-log[H+]). Pure water cannot
buffer changes in H+ concentration, so is not a buffer and
can easily be any pH, but the cytoplasms and tissue fluids
of living organisms are usually well buffered at about
neutral pH (pH 7-8).

CARBOHYDRATES

Carbohydrates contain only the elements carbon, hydrogen and

oxygen. The group includes monomers, dimers and polymers, as
shown in this diagram:

Monosaccharides

All have the formula (CH2O)n, where n is between 3 and 7. The

most common & important
monosaccharide is glucose, which is a six-carbon sugar. It's
formula is C6H12O6 and its structure is shown below

or more simply
Glucose forms a six-sided ring. The six carbon atoms are
numbered as shown, so we can refer to individual carbon atoms
in the structure. In animals glucose is the main transport sugar
in the blood, and its concentration in the blood is carefully
controlled.

There are many monosaccharides, with the same chemical

formula (C6H12O6), but different structural formulae. These
include fructose and galactose.

Common five-carbon sugars (where n = 5, C5H10O5) include

ribose and deoxyribose (found in nucleic acids and ATP).

Disaccharides

Disaccharides are formed when two monosaccharides are joined

together by a glycosidic bond. The reaction involves the
formation of a molecule of water (H2O):

This shows two glucose molecules joining together to form the

disaccharide maltose. Because this bond is between carbon 1 of
one molecule and carbon 4 of the other molecule it is called a 1-
4 glycosidic bond. This kind of reaction, where water is formed,
is called a condensation reaction. The reverse process, when
bonds are broken by the addition of water (e.g. in digestion), is
called a hydrolysis reaction.

• polymerisation reactions are condensation reactions

• breakdown reactions are hydrolysis reactions

There are three common disaccharides:

 • Maltose (or malt sugar) is glucose & glucose. It is formed
on digestion of starch by amylase, because this enzyme
breaks starch down into two-glucose units. Brewing beer
starts with malt, which is a maltose solution made from
germinated barley. Maltose is the structure shown above.
• Sucrose (or cane sugar) is glucose & fructose. It is
common in plants because it is less reactive than
glucose, and it is their main transport sugar. It's the
common table sugar that you put in tea.
• Lactose (or milk sugar) is galactose & glucose. It is found
only in mammalian milk, and is the main source of energy
for infant mammals.

Polysaccharides

Polysaccharides are long chains of many monosaccharides

joined together by glycosidic bonds. There are three important
polysaccharides:

Starch is the plant storage polysaccharide. It is insoluble and

forms starch granules inside many plant cells. Being insoluble
means starch does not change the water potential of cells, so
does not cause the cells to take up water by osmosis (more on
osmosis later). It is not a pure substance, but is a mixture of
amylose and amylopectin.
Amylose is simply poly-(1-4) glucose, so is a
straight chain. In fact the chain is floppy, and it
tends to coil up into a helix.

Amylopectin is poly(1-4) glucose with about 4%

(1-6) branches. This gives it a more open
molecular structure than amylose. Because it
has more ends, it can be broken more quickly
than amylose by amylase enzymes.

Both amylose and amylopectin are broken down by the enzyme

amylase into maltose, though at different rates.

Glycogen is similar in structure to amylopectin. It

is poly (1-4) glucose with 9% (1-6) branches. It is
made by animals as their storage polysaccharide,
and is found mainly in muscle and liver. Because
it is so highly branched, it can be mobilised
(broken down to glucose for energy) very quickly.

Cellulose is only found in plants, where it is the main component

of cell walls. It is poly (1-4) glucose, but with a different isomer
of glucose. Cellulose contains beta-glucose, in which the
hydroxyl group on carbon 1 sticks up. This means that in a chain
alternate glucose molecules are inverted.
This apparently tiny difference makes a huge difference in
structure and properties. While the a1-4 glucose polymer in
starch coils up to form granules, the beta1-4 glucose polymer in
cellulose forms straight chains. Hundreds of these chains are
linked together by hydrogen bonds to form cellulose microfibrils.
These microfibrils are very strong and rigid, and give strength to
plant cells, and therefore to young plants.

The beta-glycosidic bond cannot be broken by amylase, but

requires a specific cellulase enzyme. The only organisms that
possess a cellulase enzyme are bacteria, so herbivorous
animals, like cows and termites whose diet is mainly cellulose,
have mutualistic bacteria in their guts so that they can digest
cellulose. Humans cannot digest cellulose, and it is referred to
as fibre.

Other polysaccharides that you may come across include:

• Chitin (poly glucose amine), found in fungal cell walls and

the exoskeletons of insects.
• Pectin (poly galactose uronate), found in plant cell walls.
• Agar (poly galactose sulphate), found in algae and used
to make agar plates.
• Murein (a sugar-peptide polymer), found in bacterial cell
walls.
• Lignin (a complex polymer), found in the walls of xylem
cells, is the main component of wood.
 LIPIDS

Lipids are a mixed group of hydrophobic compounds composed

of the elements carbon, hydrogen and oxygen. They contain fats
and oils (fats are solid at room temperature, whereas oils are
liquid)

Triglycerides

Triglycerides are commonly called fats or oils. They are made of

glycerol and fatty acids.

Glycerol is a small, 3-carbon

molecule with three hydroxyl
groups.

Fatty acids are long molecules

with a polar, hydrophilic end
and a nonpolar, hydrophobic
"tail". The hydrocarbon chain
can be from 14 to 22 CH2 units
long. The hydrocarbon chain is
sometimes called an R group,
so the formula
of a fatty acid can be written as
R-
COOH.

• If there are no C=C double bonds in the hydrocarbon

chain, then it is a saturated fatty acid (i.e. saturated with
hydrogen). These fatty acids form straight chains, and
have a high melting point.

• If there are C=C double bonds in the hydrocarbon chain,

then it is an unsaturated fatty acid (i.e. unsaturated with
hydrogen). These fatty acids form bent chains, and have
a low melting point. Fatty acids with more than one
 double bond are called poly-unsaturated fatty acids
(PUFAs).

One molecule of glycerol joins togther with three fatty acid

molecules to form a triglyceride molecule, in another
condensation polymerisation reaction:

Triglycerides are insoluble in water. They are used for storage,

insulation and protection in fatty tissue (or adipose tissue) found
under the skin (sub-cutaneous) or surrounding organs. They
yield more energy per unit mass than other compounds so are
good for energy storage. Carbohydrates can be mobilised more
quickly, and glycogen is stored in muscles and liver for
immediate energy requirements.

• Triglycerides containing saturated fatty acids have a high

melting point and tend to be found in warm-blooded
animals. At room temperature they are solids (fats), e.g.
butter, lard.
• Triglycerides containing unsaturated fatty acids have a
low melting point and tend to be found in cold-blooded
animals and plants. At room temperature they are liquids
(oils), e.g. fish oil, vegetable oils.

Phospholipids

Phospholipids have a similar structure to triglycerides, but with a

phosphate group in place of one fatty acid chain. There may also
be other groups attached to the phosphate. Phospholipids have
a polar hydrophilic "head" (the negatively-charged phosphate
group) and two non-polar hydrophobic "tails" (the fatty acid
chains). This mixture of properties is fundamental to biology, for
phospholipids are the main components of cell membranes.
 • When mixed with water,
phospholipids form droplet spheres
with the hydrophilic heads facing the
water and the hydrophobic tails
facing each other. This is called a
micelle.

• Alternatively, they may form a

doublelayered phospholipid bilayer.
This traps a compartment of water in
the middle separated from the
external water by the hydrophobic
sphere. This naturallyoccurring
structure is called a liposome, and is
similar to a membrane surrounding a
cell.

Waxes

Waxes are formed from fatty acids and long-chain alcohols. They
are commonly found wherever waterproofing is needed, such as
in leaf cuticles, insect exoskeletons, birds' feathers and
mammals' fur.

Steroids

Steroids are small hydrophobic molecules found mainly in

animals. They include:
• cholesterol , which is found in animals cell membranes to
increase stiffness
• bile salts , which help to emulsify dietary fats
• steroid hormones such as testosterone, oestrogen,
progesterone and cortisol
• vitamin D, which aids Ca2+ uptake by bones.

PROTEINS

Proteins are the most complex and most diverse group of

biological compounds. They have an astonishing range of
different functions, as this list shows.
 • structure e.g. collagen (bone, cartilage, tendon), keratin
(hair), actin (muscle)
• enzymes e.g. amylase, pepsin, catalase, etc (>10,000
others)
• transport e.g. haemoglobin (oxygen), transferrin (iron)
• pumps e.g. Na+K+ pump in cell membranes
• motors e.g. myosin (muscle), kinesin (cilia)
• hormones e.g. insulin, glucagon
• receptors e.g. rhodopsin (light receptor in retina)
• antibodies e.g. immunoglobulins
• storage e.g. albumins in eggs and blood, caesin in milk
• blood clotting e.g. thrombin, fibrin
• lubrication e.g. glycoproteins in synovial fluid
• toxins e.g. diphtheria toxin
• antifreeze e.g. glycoproteins in arctic flea
• and many more!

Proteins are made of amino acids. Amino acids are made of the
five elements C H O N S. The general structure of an amino acid
molecule is shown on the right. There is a central carbon atom
(called the "alpha carbon"), with four different chemical groups
attached to it:

• a hydrogen atom
• a basic amino group
• an acidic carboxyl group
• a variable "R" group (or side chain)

Amino acids are so-called because they have both amino groups
and acid groups, which have opposite charges. At neutral pH
(found in most living organisms), the groups are ionized as
shown above, so there is a positive charge at one end of the
molecule and a negative charge at the other end. The overall
net charge on the molecule is therefore zero. A molecule like
this, with both positive and negative charges is called a
zwitterion. The charge on the amino acid changes with pH:

LOW PH (ACID) NEUTRAL PH HIGH PH (ALKALI)

charge = +1 charge = 0 charge = -1

It is these changes in charge with pH that explain the effect of
pH on enzymes. A solid, crystallised amino acid has the
uncharged structure

however this form never exists in solution, and therefore doesn't

exist in living things (although it is the form usually given in
textbooks).

There are 20 different R groups, and so 20 different amino acids.

Since each R group is slightly different, each amino acid has
different properties, and this in turn means that proteins can
have a wide range of properties. The following table shows the
20 different R groups, grouped by property, which gives an idea
of the range of properties. You do not need to learn these, but it
is interesting to see the different structures, and you should be
familiar with the amino acid names. You may already have
heard of some, such as the food additive monosodium
glutamate, which is simply the sodium salt of the amino acid
glutamate. Be careful not to confuse the names of amino acids
with those of bases in DNA, such as cysteine (amino acid) and
cytosine (base), threonine (amino acid) and thymine (base).
There are 3-letter and 1-letter abbreviations for each amino
acid.

THE TWENTY AMINO ACID R-GROUPS (FOR INTEREST ONLY NO

KNOWLEDGE REQUIRED)

SIMPLE R GROUPS BASIC R GROUPS

Glycine Lysine

Gly G Lys K

Alanine Arginine

Ala A Arg R

Valine Histidine

Val V His H

Leucine Asparagine

Leu L Asn N
 Isoleucine Glutamine

Ile I Gln Q

HYDROXYL R GROUPS ACIDIC R GROUPS

Serine Aspartate

Ser S Asp D

Threonine Glutamate

Thr T Glu E

SULPHUR R GROUPS RINGED R GROUPS

Cysteine Phenylalanine

Cys C Phe F

Methionine Tyrosine

Met M Tyr Y

CYCLIC R GROUP

Proline Tryptophan

Pro P Trp W

Polypeptides
Amino acids are joined together by peptide bonds. The reaction
involves the formation of a molecule of water in another
condensation polymerisation reaction:
When two amino acids join together a dipeptide is formed. Three
amino acids form a tripeptide. Many amino acids form a
polypeptide. e.g.:

+
NH3-Gly — Pro — His — Leu — Tyr — Ser — Trp — Asp — Lys —
Cys-COO-

In a polypeptide there is always one end with a free amino (NH 2)

(NH3 in solution) group, called the Nterminus, and one end with
a free carboxyl (COOH) (COO in solution) group, called the C-
terminus.

Protein Structure
Polypeptides are just a string of amino acids, but they fold up to
form the complex and well-defined threedimensional structure
of working proteins. To help to understand protein structure, it is
broken down into four levels:

1. Primary Structure

This is just the sequence of amino acids in the

polypeptide chain, so is not really a structure at all.
However, the primary structure does determine the rest
of the protein structure. Finding the primary structure of
a protein is called protein sequencing, and the first
protein to be sequenced was the protein hormone
insulin, by the Cambridge biochemist Fredrick Sanger,
for which work he got the Nobel prize in 1958.

2. Secondary Structure

This is the most basic level of protein folding, and

consists of a few basic motifs that are found in all
proteins. The secondary structure is held together by
 hydrogen bonds between the carboxyl groups and the
amino groups in the polypeptide backbone. The two
secondary structures are
the α-helix and the β-sheet.
The α-helix. The
polypeptide chain is wound
round to form a
helix. It is held together by
hydrogen bonds running
parallel with the long helical
axis. There are so many hydrogen bonds that this
is a very stable and strong structure. Helices are
common structures throughout biology.

The β-sheet. The

polypeptide chain zig-zags
back and forward forming a
sheet. Once again it is held
together by hydrogen bonds.

3. Tertiary Structure

This is the 3 dimensional structure formed by the

folding up of a whole polypeptide chain.
Every protein has a unique tertiary structure, which is
responsible for its properties and function. For example
the shape of the active site in an enzyme is due to its
tertiary structure. The tertiary structure is held together
by bonds between the R groups of the amino acids in the
protein, and so depends on what the sequence of amino
acids is. There are three kinds of bonds involved:

• hydrogen bonds , which are weak.

• ionic bonds between R-groups with positive or
negative charges, which are quite strong.
• sulphur bridges - covalent S-S bonds between two

cysteine amino acids, which are strong. 4. Quaternary

Structure

This structure is found only in proteins containing

more than one polypeptide chain, and simply means how
the different polypeptide chains are arranged together.
The individual polypeptide chains are usually globular,
but can arrange themselves into a variety of quaternary
shapes. e.g.:

Haemoglobin, the oxygen-carrying

protein in red blood cells, consists of
four globular subunits arranged in a
tetrahedral (pyramid) structure.
Each subunit contains one iron atom
 and can bind one molecule of
oxygen.

These four structures are not real stages in the formation of a

protein, but are simply a convenient classification that scientists
invented to help them to understand proteins. In fact proteins
fold into all these structures at the same time, as they are
synthesised.

The final three-dimensional shape of a protein can be classified

as globular or fibrous.

globular structure fibrous (or filamentous) structure

The vast majority of proteins are globular, including enzymes,

membrane proteins, receptors, storage proteins, etc. Fibrous
proteins look like ropes and tend to have structural roles such as
collagen (bone), keratin (hair), tubulin (cytoskeleton) and actin
(muscle). They are usually composed of many polypeptide
chains. A few proteins have both structures: the muscle protein
myosin has a long fibrous tail and a globular head, which acts as
an enzyme.

This diagram shows a molecule of the enzyme This diagram

shows part of a molecule of collagen, dihydrofolate reductase,
which comprises a single which is found in bone and cartilage.
It has a polypeptide chain. It has a globular shape unique,
very strong triple-helix structure. It is a fibrous protein
 Biochemical Tests

Benedicts test for reducing sugars

• grind up sample
• add Benedicts solution
• heat
• colour change from blue to red/brown indicate reducing
sugars
• note simple non reducing sugars (mainly disaccharides)
can all be hydrolysed to their reducing sugar components
by heating with dilute acid (e.g. HCl). If you neutralise
after heating you can then perform the Benedicts test
• a positive result indicates the presence of a simple non-
reducing sugar

Iodine (I2) test for starch

• add drops of Iodine to sample

• colour change from brown to blue black indicates
presence of starch
 Shultz's test for cellulose

• add Shultz's solution

• purple colour indicates presence of cellulose

Biuret test for protein

• grind up sample
• add Biuret solution
• lilac colour indicates protein present

Emulsion test for lipids

• grind up sample
• add ethanol
• decant into water
• cloudy emulsion indicates presence of lipid

LIPID
CHARACTERISTIC PROTEINS CARBOHYDRATE

Elements present CHON CHO CHO

Type of bond Peptide Glycosidic Ester

Reagent in Tests Biuret Benedict Ethano

Glycerol/Fat
Simplest form Amino Acids Monosaccharide

How bonds formed Condensation Condensation Condensation

How bonds broken Hydrolysis Hydrolysis Hydrolysis

Formation of long chains

Polypeptides Polysaccharide None

Polar Yes Yes No

Type of polarity Hydrophilic Hydrophilic Hydrophobic

Dissolve in water Yes Yes Basically No

CARBOHYDRATES - KEY NOTES

Contain Elements: Carbon, Hydrogen and Oxygen.
Biological

Importance…
Energy Source Carbohydrates are principal respiratory substrates
Structural
Compounds Cellulose (CW of all plant cells) & Lignin
Storage Plants, Starch (common plant storage never in animals) Animals.
Compounds Glycogen (e.g. mammalian liver)
CLASSIFICATION: The basic sugar unit = the saccharide

• 1 sugar unit = Monosaccaride

• 2 sugar units = Disaccharide
• Many sugar units = Polysaccharide

MONOSACCHARIDES
Examples of Monosaccharides: Glucose, Ribose

General There are the building blocks of other important C/H’s

Monosaccharides are:

• Sweet tasting
• Soluble in water
• Reducing sugars (see below)

Reducing Sugar Properties (all monosaccharides are reducing

sugars). M/S are capable of REDUCING benedicts solution. When
this reduction occurs benedicts solution changes from blue to
orange/red.

DISACCHARIDES
Examples of D/S: Maltose (Malt sugar), Lactose (milk sugar)

Maltose formed by CONDENSATION of 2 units of glucose, the

bond is called a glycosidic bond.

Note: In the exam you could be given half of the reaction

below and asked to fill in the other half - you wouldn't be
asked to come up with it all off the top of your head

2 molecules of glucose
 +
Undergo a condensation reaction to form…

+
H2O
Maltose and Water

General Summary of disaccharides

• May be non-reducing
• Sweet tasting
• Water soluble

POLYSACCHARIDES
Examples of P/S: Starch, Glycogen, Cellulose

These are an important group of carbohydrates. Two main

divisions:

• Structural Polysaccharides e.g. Cellulose, Chitin, Lignin

(wood)
• Storage Polysaccharides e.g. Starch and Glycogen

General Properties of P/S

• Non sweet tasting

• Non truly soluble in H2O
Structural P/S

In these polysaccharides the sugar unit residues present in long

chain molecules of the polymer are straight, and cross-linkages
between chains occur giving the material its strength.