IB Higher Options - B Human Bio Chemistry PDF

B Human biochemistry
B1 Energy
All living things require the input of energy to exist this energy is used
to drive the thousands of biochemical reactions that occur to allow the
organism to grow, reproduce and sustain life. This energy comes almost
always from the Sun, in the first instance energy from sunlight is
captured by photosynthetic organisms (e.g. plants, algae, certain bacteria)
and converted into carbohydrates. These are then broken down by a
process called cellular respiration, to produce energy-rich molecules
(e.g. adenosine triphosphate, or ATP) that release energy to drive
biochemical reactions. Photosynthetic organisms can by ingested by nonphotosynthetic animals, and the carbohydrates (and other biomolecules)
can be broken down and used for cellular respiration.
As we ourselves are non-photosynthetic organisms, we must obtain
our energy through what we ingest, i.e. via our diet, so that our cells are
able to carry out all the necessary biochemical reactions. The amount of
energy required by an individual will depend on the amount of physical
activity they perform, but in general an average man requires about 10 500
kilojoules (kJ), equating to 2500 kilocalories (kcal) per day, while an
average woman needs approximately 8400 kJ (2000 kcal) per day.
The amount of energy found within different foods we buy is often
displayed on the food packaging. This energy value is worked out through
a process known as food calorimetry. A food (or bomb) calorimeter can be
used, which measures the heat of combustion. Here, a known mass of a
particular food is ignited and completely burnt in the presence of oxygen.
The energy released is transferred to water and the rise in temperature
of the water is measured. The energy contained in the food can then be
calculated using the following equation:
Learning objectives
Calculate the energy value

of food using enthalpy of
combustion data
1 kJ = 0.24 kcal
q = mcT
where:
q = heat evolved (J)
m = mass of water (g)
c = specific heat capacity of water (4.18 J g1 K1 or 4.18 J g1 C)
(This is included in the IBO Chemistry Data booklet.)
T = temperature change of the water (in C or K)
Worked example
When 1.00 g of tomato soup was burnt in a food calorimeter containing 100 g water, it raised the temperature of
the water from 20.4 C to 28.0 C. Calculate the energy content of 100 g of tomato soup.
From the equation q = mcT, for 1.00 g of tomato soup, we know that:
m = 100 g
c = 4.18 J g1 K1
T = 28.0 20.4 = 7.6 C (which is 7.6 K, as it is the change in temperature that we are looking at, not the actual
temperature).
CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011
B HUMAN BIOCHEMISTRY
Therefore:
q = 100 4.18 7.6 = 3176.8 J, i.e. 3.18 kJ per 1 g
So, in 100 g of tomato soup, there will be 3.18 100 = 318 kJ.
Examiners tip
You could also be told the
heat capacity of the whole
system (water and calorimeter
together) and asked to work
out the enthalpy change. In
that case, in the first step you
just multiply the heat capacity
by the temperature change.
This method does not account for the heat lost through the
container. The heat capacity of the thermometer and container of
the food calorimeter must also be taken into account to increase
accuracy of the results.
Test yourself
1 Complete combustion of 2.50 g of a snack food raised the
temperature of 200.0 g of water by 17.9 C. Calculate the energy
value per 100 g of the food.
2 10.0 g of a biscuit was completely combusted in a food
calorimeter. The heat capacity of the whole system was
8.50 kJ C1, and the temperature of the system increased
12.1 C. Calculate the energy value of 100 g of the biscuit.
3 If 100 g of cooked rice contains 530 kJ energy, by how many
degrees Celsius does the water temperature rise when 1 g of
cooked rice is completely burnt in a food calorimeter containing
100 g water?
Learning objectives
Draw the general structure of

a 2-amino acid and identify
the different functional groups
within the molecule
Describe how amino acids
behave under different pH
values
Describe how amino acids join
together to form peptides
Describe the primary, secondary,
tertiary and quaternary
structures of proteins and
explain the bonding and
interactions that occur between
the amino acids within these
structures
Note the different types of
proteins in the human body and
their function
Discuss the various analytical
methods used to identify
proteins
B2 Proteins
Structure of amino acids
Amino acids are the building blocks (monomers) of which proteins
(polypeptides) are made up. There are 20 naturally occurring 2-amino
acids that make up proteins in the body. These link together to form
chains, and it is the sequence of these 2-amino acids in the chain that
determines the overall structure (and therefore function) of the protein.
These 2-amino acids have a common structure (Figure B1): they consist
of a central carbon atom to which are attached four groups:
1 a carboxylic acid (COOH)
2 an amine (NH2)
3 a hydrogen (H)
4 An R group (this is different in each of the 20 amino acids)
H
H2N
COOH
R
Figure B1 General structure of a 2-amino acid.
The general chemical formula of a 2-amino acid can be written as:

HOOCC(R)HNH2
These compounds are called 2-amino acids because the amino group is
on carbon 2, counting the C of the carboxylic acid group as carbon 1. For
example, the amino acid shown in Figure B2 is called 2-aminoethanoic
acid.
Acidbase behaviour of 2-amino acids

Amino acids contain both acidic and basic groups in the same molecule
they are thus amphoteric.
Amines can accept a proton:
amine (amino)
group
O
1
C
O
carboxylic
acid
Figure B2 Diagram showing the numbering

on the C atoms in an amino acid.
RNH2 + H+ RNH3+
Carboxylic acids can donate a proton:
RCOOH RCOO + H+
The carboxylic acid group can protonate an amino group in the same
molecule. When the proton is transferred from the COOH to the NH2, a
neutral ion is formed, as it bears no net charge, and this neutral form of
the amino acid is known as a zwitterion (Figure B3).
H
N
H
transfer of proton
H
H N+
H
C
The central carbon atom is also

sometimes referred to as an
-carbon, as it is next to (known
as to) a carboxylic acid group.
Therefore in some texts, 2-amino
acids are called -amino acids.
The word zwitterion comes

from the German word for
hermaphrodite.
R
zwitterion
Figure B3 Formation of a zwitterion.
The pH at which this zwitterion exists is known as the isoelectric

point (Figure B4) and will differ depending on the R group attached
to the amino acid. This difference in isoelectric point can be exploited
analytically, as it is used to separate different proteins and amino acids (see
Electrophoresis on page 10).
When the pH of an amino acid in solution is altered, the charges on
the amino acid change:
The amine group is basic and therefore, at low pH, picks up a proton
in acidic and neutral conditions and exists as the NH3+ group.
However, as the pH is increased and the solution becomes basic, the
ammonium ion loses its proton and exists in the unionised (NH2)
form (Figure B4).
As the pH increases, the carboxylic acid loses its proton and exists in
the ionised carboxylate (COO) form.
H
H3N+
low
pH
COOH
H3N+
COO
H2N
cation
zwitterion
anion
COO
isoelectric
point
high
pH
Figure B4 Changes in charges on the amino acid as pH increases.
Amino acids can act as buffers
A buffer solution is one that resists

changes in pH when small amounts
of acids and alkalis are added.
We mentioned above that amino acids are amphoteric, i.e. they contain both
acidic and basic groups and can therefore act as either an acid or a base.This
is an important property of amino acids, as it allows them to act as buffers.
The key reason that the buffering occurs is that the amino acids have
groups that can react with H+ or OH. Any acid (H+) added is mopped
up by either the COO or NH2 groups (depending on the pH) and any
base (OH) added is mopped up by reaction with the COOH or NH3+
groups. It is, therefore, possible for the pH to remain fairly constant.
Amino acids play an important role in buffering the aqueous
environment within cells. Significant changes in cellular pH can have a
disastrous effect on the biochemical reactions that take place there, as they
prevent enzymes, which usually only work within narrow pH ranges, from
carrying out their catalytic activity. Proteins may also change shape in low
or high pH and thus lose their function.
The full explanation is a bit

more complicated than this, and
the various species present in
equilibrium must be considered.
Examiners tip
Buffer solutions are not part
of the core Standard Level
syllabus, but if you would like
to learn a bit more about them,
they are covered in the Higher
Level section of Chapter 8 on
page 359 of the Coursebook.
The systematic name of glycine is

2-aminoethanoic acid, and we have
seen it already in Figure B2.
Types of amino acid

There are 20 naturally occurring 2-amino acids and therefore 20 different
R groups. The simplest 2-amino acid is called glycine (abbreviated to
Gly), where R = H. The other 19 amino acids can be grouped according
to whether their R group is neutral, acidic or basic.
HL
Extension
All the 2-amino acids except glycine are optically active, as they possess a
chiral centre.
An example of an acidic amino acid is aspartic acid (Asp), which
has the R group CH2COOH. An example of a basic amino acid is
lysine (Lys), where R = CH2CH2CH2CH2NH2. Neutral amino acids
bear neutral R groups, for example R = CH3 (alanine, Ala), R = CH2SH
(cysteine, Cys) and R = CH2OH (serine, Ser).
Structure of proteins
Proteins are chains of amino acids linked together. There are estimated to
be approximately a million different proteins in the body, and these differ
only in the number and sequence of amino acids in their chains. As
we shall see, the sequence of amino acids determines the overall structure
(and therefore function) of the protein; it allows the protein to exist in a
particular shape, this shape being maintained by bonds and forces between
the different amino acids in the chain.
The precise linear sequence of amino acids in the polypeptide
chain is known as the primary structure of the protein, for
example:
GlyLysCysGlySerAlaAla
(glycinelysinecysteineglycineserinealaninealanine)
Amino acids join together to form a chain in a condensation reaction.
The general reaction to form a dipeptide (two-amino acid chain) is shown
in Figure B5.
4
H
H2N
H
COOH + H2N
H2N
Condensation reaction: two

molecules join together with the
elimination of water.
COOH
H
N
COOH + H2O
peptide
bond
Figure B5 Condensation reaction between two amino acids to form a dipeptide and
water.
A covalent bond is formed as the carboxyl end of one amino acid reacts
with the amino end of the other amino acid, and a molecule of water is
lost (hence the term condensation reaction). The group that links the
two amino acids is an amide, and this linkage is called a peptide bond
in proteins.
When two different 2-amino acids react together, two different
dipeptides can be formed (Figure B6).
H
H2N
COOH + H2N
CH2OH
H2N
alanine
CH3
alanine
COOH + H2N
H2N
CH3
serine
COOH
CH2OH
The amide functional group is:

O
C
N
H
H
N
CH3
COOH + H2O
Ser-Ala
COOH
H2N
CH2OH
serine
CH3
COOH + H2O
CH2OH
Ala-Ser
Figure B6 Formation of two possible dipeptides.
The dipeptides are different depending on which way around the

amino acids are joined together. The first dipeptide in Figure B6 is
formed when the acid group of serine reacts with the amino group of
alanine. The second dipeptide is formed when the amino group of serine
reacts with the acid group of alanine.
The general reaction to form a chain consisting of three amino acids (a
tripeptide) is shown in Figure B7.
When we write the sequence of amino acids in the chain, it is
important to avoid confusion, with everyone starting from the same end
of the polypeptide chain. By convention, peptide chains are always named
by starting at the amino end of the chain; hence the sequence for the
tripeptide in Figure B8 would be written as GlyCysSer.
H2N
H
N
H2N
H
COOH + H2N
COOH
peptide
bond
H
N
COOH + H2O
peptide
bond
Figure B7 Condensation reaction between a dipeptide and an amino acid to form a

tripeptide and water.
Five other tripeptides could be

formed from reacting glycine,
cysteine and serine: GlySerCys,
CysGlySer, CysSerGly,
SerCysGly and SerGlyCys.
amino end
H2N
CH2SH
Gly
carboxyl end
CH2OH
Cys
COOH
Ser
Figure B8 Structure of the tripeptide GlyCysSer.
Secondary structure of proteins

Proteins do not normally exist as linear chains they usually contain
stretches in which the chain folds into regular patterns known as
-helices and -pleated sheets (Figure B9). This is known as the
secondary structure of a protein.
The -helix
The -helix is a helix that twists in a clockwise direction, with each
complete turn consisting of 3.6 amino acids it can be likened to
a corkscrew. The helical structure is stabilised (i.e. held in shape) by
H
N
H
O
C
O
N
H
H
C
hydrogen bonds
R
H
H
C
O
C
N
H
C
R
R
a -helix (only some
of the amino acids have
been shown)
H
C
R
N
H
O
C
C
H
R
C
H
R
H
C
H
C
O
C
R
N
H
H
N
N
H
C
H
R
C
H
H
C
C
R
H
N
H
C
O
C
R
b -pleated sheet
Figure B9 (a) -helix; (b) -pleated sheet.
hydrogen bonds between the carbonyl C=O of one peptide bond and
the NH of the peptide bond four amino acids below it. These hydrogen
bonds are known as intramolecular hydrogen bonds, as they exist
between atoms within the same peptide chain.
The -pleated sheet

-pleated
sheets consist of two or more stretches of amino acids in which

the polypeptide chain is almost fully extended they take on a pleated
appearance, hence the name. Intramolecular hydrogen bonds form
between a C=O on one strand and an NH on an adjacent strand, which
stabilises the structure.
Tertiary structure of proteins

Each polypeptide molecule has a specific three-dimensional shape, and
this is known as the tertiary structure of the protein. The tertiary
structure exists because of a number of interactions between R groups
(side chains) of amino acids in the polypeptide chain (Figure B10), which
hold the polypeptide in a particular shape. These interactions include:
hydrogen bonds between amino acids bearing side chains containing,
for example, OH and N
van der Waals forces between amino acids bearing hydrophobic/
non-polar side chains
electrostatic forces/ionic bonds between, for example, COO and
NH3+ containing side chains
disulfide bonds (bridges): covalent SS bonds formed by the
oxidation of sulfhydryl (SH) groups within two cysteine residues.
The function of the protein depends on its shape, and the shape of the
protein depends on the interactions formed between the amino acids in
the polypeptide chain.
The precise sequence of amino

acids is vital to the function
of the protein changes in
the sequence can result in loss
of important interactions and
therefore a change in the overall
shape.
Tyr
H2C
Val
CH
H3 C
hydrogen
bonding
H+
CH3
H 3C
CH3
van der Waals

interactions
CH
Val
HN
Lys
H2C
His
Cys
CH2
S disulfide
S
bridge
+NH3
O
CH2
Cys
ionic bonding
CH2
Asp
Figure B10 The different types of interactions that can occur between some amino
acids in the peptide chain.
Quaternary structure of proteins

Many proteins are made up of more than one polypeptide chain. These
chains are referred to as polypeptide sub-units and associate in a specific
manner this is known as the quaternary structure.
The sub-units may be held together by various intermolecular
interactions (i.e. interactions between groups in different protein chains),
including hydrogen bonds, ionic interactions, van der Waals forces and
disulfide bonds. Proteins made up of two sub-units are known as dimers,
those with three sub-units are called trimers and those with four subunits are known as tetramers. The sub-units may be identical to each
other or may be different in structure.
Examples of tetramers containing two types of sub-units are
haemoglobin and immunoglobulin G, an antibody with wide
immunological action in the body.
Functions of proteins
Proteins serve a variety of functions in the body. These are summarised in
Table B1.
Analysis of proteins
There are various analytical techniques that can be used to identify
proteins and amino acids. Here we will focus on two: paper
chromatography and electrophoresis.
Paper chromatography
This is a simple method for identifying the composition of amino acids in
a particular protein.
The protein must first be broken down into its constituent amino acids,
and this is usually carried out by the addition of acid, such as heating
Function
Comments
Examples
structural
provide support and strength
collagen (most abundant protein in body;

found in tendons, cartilage, skin, bones),
keratin (found in hair and nails)
biological
catalysts
enzymes catalyse biochemical reactions within the body
salivary amylase (involved in starch digestion),

DNA polymerase (joins nucleotides together
to form DNA), etc. (there are thousands of
different enzymes in the body!)
hormones
have a regulatory effect on specic cells/organs in the body
insulin (regulates blood glucose levels), growth

hormone (regulates growth and cellular
reproduction)
immunological play a key role in the ght against infection

proteins
antibodies (recognise and bind to foreign

antigen)
transport
carry materials around the body
haemoglobin (transports oxygen), serum

albumin (transports many substances, such as
fatty acids, certain hormones)
energy source
proteins are broken down to amino acids in the body, which

can enter the citric acid cycle to generate ATP (a highenergy molecule used to fuel biochemical reactions)
Table B1 Functions of proteins in the body.
with 6 mol dm3 HCl. The acid hydrolyses the protein by breaking
the peptide bonds between the amino acids. A small sample of the
resultant mixture of amino acids can then be spotted onto a piece of
chromatographic paper and separated by placing the paper into a tank
containing a suitable solvent (Figure B11).
tank
solvent front
9.2cm
6.7cm
3.9cm
pencil line
solvent
sample
This is also discussed in Option A

on the CD-ROM, pages 3033.
Figure B11 Separation of amino acids using paper chromatography.
The solvent rises up the paper by capillary action and, as it does so,
the amino acids travel up the paper. The extent to which each amino
acid travels up the paper is dependent on how it partitions between the
stationary phase (the water in the chromatographic paper) and the mobile
phase (the solvent), and this is dependent on its relative solubility in each
of the two phases. For example, if an amino acid is more soluble in the
water (stationary) phase than the solvent (mobile) phase, it will travel less
distance up the paper than if it was more soluble in the solvent phase.
If the amino acid is highly soluble in the mobile phase, then it will rise
higher up the paper.
Once the solvent has risen to almost the top of the paper, the paper is
removed from the tank. It is important to mark the distance travelled by
the solvent front as soon as the paper is removed, so that the retardation
factor (Rf) can be calculated. Before the Rf values can be determined,
the paper must be sprayed with ninhydrin (a locating agent) this colours
the amino acids purple and allows them to be visualised. Each amino acid
appears as a small spot on the paper.
The next step is to measure how far each spot has travelled up the
paper (distance from the pencil line to the middle of the spot) and then
divide this distance by the distance travelled by the solvent front (distance
from original pencil line) this calculation will give you the Rf value for
that particular spot:
Rf =
distance travelled by spot

distance travelled by solvent front
The Rf value is always 1 or less.
Each amino acid has a characteristic Rf value when run under the same
conditions and therefore can be identified by comparing the Rf value of
the spot with the Rf values of known amino acids.
Examiners tip
If your answer is greater than
1, then you know that you
have gone wrong somewhere.
The Rf value does not have units.
To give an example, in Figure B11, the distance to the top spot is

measured and found to be 6.7 cm; the solvent front has travelled 9.2 cm
from the line at which the sample was spotted. Therefore:
Rf =
6.7
= 0.73
9.2
Amino acids can also be identified by spotting known amino acids on the
paper alongside the unknown sample if a particular amino acid travels
the same distance up the paper as a known one, it can be identified.
Electrophoresis
Another way of analysing amino acids and proteins is using a technique
called electrophoresis. This technique separates charged molecules based
on their ability to migrate when an electric field is applied to the
system.
Both proteins and amino acids can be analysed using this technique. If
the amino acid composition of a protein is to be investigated, the protein
is first treated with acid (as with paper chromatography) to hydrolyse
the peptide bonds between the amino acids. The sample mixture is then
applied to a support, such as paper or a polymer gel (polyacrylamide is
the most common), which is saturated with a buffer of a certain pH, used
as the conducting liquid. An electric field is applied across the support,
and those amino acids bearing negative charges at the buffer pH migrate
to the positive electrode (anode), whereas those bearing a positive charge
migrate to the negative electrode (cathode). Those amino acids with no
net charge remain stationary. Detection of the amino acids is usually by
staining.
So what dictates the charge found on the amino acid at the buffer
pH? The answer is its isoelectric point. We have already seen that the
isoelectric point is the pH at which the amino acid exists in the neutral
(zwitterion) form (see page 3). Remember that the different amino acids
have different isoelectric points, depending on the R group attached
to the central carbon. If you place an amino acid into a solution at a
pH above its isoelectric point, the amino acid will carry a net negative
charge and move towards the positive electrode; if the amino acid is in a
solution with a pH below its isoelectric point, it will bear a net positive
charge and move towards the negative electrode. Therefore, a mixture of
amino acids can be separated in an electric field at a certain pH due to the
differences in their isoelectric points. Mixtures of whole proteins can also
be separated, most commonly using a polymer gel as the support medium.
Test yourself
4 2-amino acids contain both basic and acidic groups
attached to the central carbon. Name the basic group
and the acidic group common to all 2-amino acids.
5 Draw the tripeptide AlaGlyCys.
7 The isoelectric point for alanine is at pH 6.15.

If alanine were placed into a buffer solution of
pH 4.0 and an electric field applied, would alanine
move towards the anode or cathode?
6 If an amino acid has an Rf value of 0.92, is it likely

to be more soluble in the mobile phase or the
stationary phase?
10
B3 Carbohydrates
Learning objectives
Carbohydrates are widespread in nature and are, in fact, the most abundant
class of biological molecules. They range from simple sugars, such as
glucose and fructose, to more complex carbohydrates, such as starch and
cellulose. The simplest of the carbohydrates are known as monosaccharides
these can exist on their own or can join together to form polymers
known as polysaccharides.
Carbohydrates have a number of functions in the human body,
for example:
as an energy source glucose is converted into ATP to drive
biochemical reactions
as an energy store glucose is polymerised into glycogen and
stored for times when blood glucose levels fall and energy is
needed
as a precursor for other biomolecules such as nucleic acids.
Structure of monosaccharides
The smallest monosaccharides contain just three carbons and are known
as trioses. We will, however, concentrate on those monosaccharides that
contain six carbons the hexoses. Examples of hexoses are glucose and
fructose; both these sugars have the same molecular formula (C6H12O6),
but have different structural formulas. They can exist in either the straight
chain form or the cyclic form (Figure B12).
Glucose contains an aldehyde group and is known as an aldose,
whereas fructose contains a ketone group and is known as a ketose sugar.
The ring form of monosaccharides

In solution, the straight-chain form of the monosaccharide cyclises into a
ring structure. This happens when the carbon with the double-bonded O
Describe the common structural

features of monosaccharides
and draw the straight-chain and
ring-closed forms of glucose and
fructose
Describe the different
disaccharides and
polysaccharides that can be
formed through condensation
reactions of monosaccharides
Briefly describe the main
functions of carbohydrates in the
human body
Describe the structural
differences and similarities
between starch and cellulose and
explain why humans are able to
digest starch but not cellulose
Briefly describe what the
term dietary fibre means and
discuss why an adequate intake
is important for health and
prevention of disease
Monosaccharides have the

empirical formula CH2O. They
contain a carbonyl group (a
ketone or aldehyde) and have
at least two hydroxyl (OH)
groups as part of their structure.
aldehyde
O
H
1
CH2OH
OH
HO
C
C
C
C
C O ketone
HO
OH
OH
OH
OH
CH2OH
fructose
CH2OH
glucose
CH2OH
H
4
OH
H
OH
3
CH2OH
H
OH
CH2OH
O
OH
OH
OH
H
H
OH
Figure B12 Straight chain and ring structures of glucose and fructose.
11
CH2OH
5
H
OH
H
OH
OH
H
1
OH
Disaccharides
glucose
CH2OH
5
H
OH
H
OH
OH
(carbon 1 in glucose) joins to carbon 5 via a bridging O atom. However,

this can happen in two ways, so that when an OH group is formed on
carbon 1 it can either be on the same side of the ring as the CH2OH
group on carbon 5 (-isomer) or on the opposite side of the ring
(-isomer) (Figure B13).
OH
1
glucose
Figure B13 Structures of -glucose and

-glucose. In the -isomer the OH is below
the ring and on the opposite side of the ring
to the CH2OH group; in the -isomer the OH
is above the ring and on the same side of
the ring as the CH2OH group.
When two monosaccharides join together, they form a disaccharide.This is

an example of a condensation reaction, when two molecules join together
with the elimination of water.This results in the formation of a glycosidic
linkage between the two sugars (Figure B14).When the linkage is
formed between the C1 of an -sugar molecule and the C4 of another sugar
molecule, it is known as an -1,4-glycosidic linkage (or bond).
Examples of common disaccharides are maltose (one of the products
from the digestion of starch is made up of glucose + glucose), lactose
(a major sugar found in milk, which is a disaccharide of
glucose + galactose) and sucrose (common table sugar, made up of
glucose + fructose).
CH2OH
CH2OH
H
OH
H
OH
O
H
OH
H
4
OH
OH
H
OH
H
CH2OH
CH2OH
H
OH
H
H
1
OH
glucose
O
H
4
OH
H
OH
glucose
O
H
OH
O
1,4 glycosidic
linkage
H
OH
H
1
+H2O
OH
OH
maltose
Figure B14 The condensation reaction between two glucose monosaccharides to
produce maltose, a disaccharide.
Polysaccharides
Polymers of many monosaccharides joined together are known as
polysaccharides. Examples include starch (polymer of -glucose sugars),
glycogen (polymer of -glucose sugars) and cellulose (polymer of
-glucose sugars). Note that all these polysaccharides are polymers of
glucose.
Plants convert excess glucose into starch for storage, and starch consists
of a mixture of two types of glucose polymers, called -amylose and
amylopectin. -amylose consists of thousands of -glucose units linked
together to form linear, unbranched chains. These glucose units are linked
by -1,4-glycosidic linkages (Figure B15a). Amylopectin is a branched
polymer of -glucose units linked by -1,4 glycosidic linkages and -1,6glycosidic linkages at the branch points (Figure B15b). Starch is present
as starch grains within plant cells, and these can be easily seen under a
microscope when stained blue-black using iodine.
12
We have digestive enzymes that are able to hydrolyse the -1,4 and
linkages within starch, and hence we can break down the starch
polymers into smaller pieces and eventually into single glucose units, which
can then be absorbed into the bloodstream and used as an energy source.
Just as plants store their excess glucose in the form of starch, we store
our excess glucose in the form of glycogen. Glycogen bears similarities
to the structure of amylopectin, in that it is a branched polymer of
-glucose units linked by -1,4-glycosidic linkages and -1,6-glycosidic
linkages. It is more highly branched than amylopectin and is stored
as granules within cells in particular, liver and skeletal muscle cells.
Glycogen is digested back into glucose when energy is needed.
Cellulose, found in plant cell walls, is a polysaccharide responsible
for giving structure and strength to plants examples include wood and
cotton. It, too, is made up of glucose units, but in this case, the glucose
units are in the form of -glucose, i.e. the OH is on the same side of the
ring as the CH2OH. This means that the glycosidic linkages between the
glucose units are also and are known as -1,4-glycosidic linkages (Figure
B16).
The glucose units in cellulose are linked by -1,4-glycosidic linkages;
we do not possess the enzyme (known as cellulase) that hydrolyses these
linkages, and therefore we (and most other animals) cannot digest cellulose.
Certain plants have a high starch

content within their cells: for
example, potato tubers, rice grains
and wheat. These are the major
sources of carbohydrate in the
human diet.
-1,6
O
H
OH
OH
1,4glycosidic
linkage
O
H
OH
CH2OH
CH2OH
CH2OH
CH2OH
Note that cellulose is made up of

linear chains and is not branched.
The polymer chains lie side by side
and form many hydrogen bonds
between glucose units within the
chains and between the chains,
giving the cellulose structure its
strength.
OH
1,4glycosidic
linkage
O
H
OH
H
H
OH
H
O
1,4glycosidic
linkage
O
H
OH
OH
a amylose
CH2OH
CH2OH
H
OH
H
OH
O
H
O
1,4glycosidic
linkage
1,6glycosidic
linkage
OH
CH2OH
CH2
O
H
OH
CH2OH
O
H
OH
H
OH
OH
CH2OH
H
OH
H
O
1,4glycosidic
linkage
O
H
OH
H
H
OH
H
O
1,4glycosidic
linkage
O
H
OH
OH
b amylopectin
Figure B15 Examples of how the glucose units are joined in (a) amylose and (b) amylopectin.
13
CH2OH
H
OH
H
1,4glycosidic
linkage
OH
H
O
CH2OH
OH
CH2OH
OH
H
OH
1,4glycosidic
linkage
O
H
OH
OH
H
O
CH2OH
OH
cellulose
Figure B16 Glucose units joined together in cellulose.
Herbivores such as cows survive

on a diet of cellulose-rich plants
such as grass. These animals have
an extensive digestive system
that contains bacteria that secrete
cellulase, and this allows the
breakdown of cellulose into smaller
units for digestion.
Dietary bre
Dietary fibre is plant material that we ingest but are not able to digest.
It passes through the gut relatively intact, as we do not possess cellulase
enzymes capable of hydrolysing it.
There are two types of dietary fibre.
1 Insoluble fibre: this includes cellulose, hemicellulose and lignin
found in plant cell walls. As it passes through the gut, it binds water
and softens and adds bulk to the faeces. Dietary sources include whole
grains (such as wheat), vegetables and beans.
2 Soluble fibre: this includes pectin found in plant cells; sources include
oats, oatbran and beans.
Dietary fibre has been linked to having a beneficial effect on a number of
conditions/diseases:
a high-fibre diet is useful in treating and preventing constipation,
haemorrhoids and diverticulosis (formation of small pouches in the
colon) and may improve some cases of irritable bowel syndrome (IBS)
Crohns disease is a condition caused by inflammation of the bowel
wall; a diet high in fibre is one form of treatment for this condition
a high-fibre diet may help in overcoming obesity, as fibre provides bulk
to a meal yet contains relatively few calories, as it is not digested
soluble fibre has been shown to reduce cholesterol levels by lowering
LDL (see page 21); therefore, a diet rich in soluble fibre has been linked
to having a beneficial effect on reducing the incidence of heart disease
fibre, especially soluble fibre, has been shown to slow the absorption of
glucose and thus lead to a lowering of blood glucose levels; it may thus
lower the risk of developing diabetes mellitus.
Test yourself
8 Is the following sugar an -sugar or a -sugar?
CH2OH
H
OH
O
H
OH
H
9 A disaccharide is shown below. State the type of

reaction that resulted in its formation and name
the linkage between the two rings.
H
OH
CH2OH
H
OH
OH
14
CH2OH
O
H
OH
OH
H
O
O
H
OH
OH
OH
H
B4 Lipids
The word lipid comes from lipos, the Greek word for fat. There are
various types of lipid in the human body: for example, steroids (e.g.
cholesterol, a steroid that is abundant in cell membranes and also is a
precursor for many steroid hormones), triglycerides (found in fatty
(adipose) tissue and act as an energy store) and phospholipids (found in
cell membranes). These three lipids have something in common they
are all hydrophobic in nature and thus are not soluble in water; they are,
however, soluble in non-polar or weakly polar organic solvents such as
trichloromethane (CHCl3) and ethoxyethane (CH3CH2OCH2CH3).
Lipids are hydrophobic molecules that contain carbon, hydrogen
and oxygen in various proportions (the predominant atoms
are carbon and hydrogen, and therefore the chains are nonpolar); some types of lipid can also contain other atoms such as
phosphorus and nitrogen (in phospholipids).
Learning objectives
Triglycerides
Tricglycerides are the most abundant class of lipids and make up the
majority of lipids in the diet; fats and oils consist of triglycerides. Fat
(as triglycerides) is found in cells known as adipocytes, which make up
adipose (fatty) tissue. Adipose tissue has a number of roles in the body: it
acts as a major energy reserve; it provides insulation from heat loss through
the skin; and it insulates, protects and supports organs such as the heart
and kidneys.
Fat is an important energy store in the body, as it has a higher energy
value than carbohydrate or protein. In other words, more energy is
released per gram of fat than per gram of carbohydrate or protein. Energy
is obtained from food in a process called cellular respiration. This is where
food molecules, such as fat (as fatty acids) and carbohydrates (as glucose)
are oxidised by a series of enzyme-catalysed reactions to ultimately
produce carbon dioxide and water. The carbon atoms in fatty acids are
less oxidised than in carbohydrates or protein, and thus they are able to
undergo more oxidation, resulting in the release of more energy.
Triglycerides are non-polar, hydrophobic molecules. They are formed
by condensation of three fatty acids with the three alcohol groups of
glycerol (propane-1,2,3-triol) (Figure B17). The functional group formed
is an ester group, and so this reaction can also be called esterification.
Compare the structures of

triglycerides, steroids and
phospholipids
Describe the condensation of
glycerol and free fatty acids to a
triglyceride
Explain why fats are higher in
energy than carbohydrates
Define the term iodine number
and use addition reactions to
calculate the number of carbon
carbon double bonds in an
unsaturated fat/oil
differences between saturated and
unsaturated fatty acids and explain
how the composition of fats is
related to their melting point
Describe the structures of the
omega-3 and omega-6 essential
fatty acids and discuss their
importance to health
Explain the differences between
the structures and function of
HDL- and LDL-cholesterol
and outline their role in the
development or prevention of
disease
Describe the digestion of
triglycerides
Discuss the roles of lipids in the
body and their impact on health
and disease
Fats yield approximately 37 kJ energy per gram, whereas

carbohydrates and protein yield approximately 16 kJ per gram each.
15
removal of water
CH2
HO
C
O
CH
HO
C
O
CH2
glycerol
Triglycerides are not usually made

up of the same fatty acid they
usually contain different fatty acids.
Fatty acids contain a long

hydrocarbon chain with a
carboxylic acid (COOH) at
one end. They have the general
formula: CH3(CH2)nCOOH.
cis and trans (geometrical)

isomerism is not covered on the
Standard Level core syllabus. See
the Higher Level part of Chapter
10 on page 487 of the Coursebook
for more detail on this.
16
fatty acids
O
CH2
Examiners tip
The esterification reaction
is not on the Standard Level
syllabus. See the Higher Level
section of Chapter 10 on
page 471 of the Coursebook
for further details of
esterification.
HO
C
O
CH
C
O
CH2
ester linkages
+ 3H2O
triglyceride
Figure B17 Condensation of glycerol with three fatty acids to form a triglyceride,
where R, R and R are long-chain hydrocarbons. Each individual reaction is a
condensation reaction and results in the elimination of water.
Fatty acids
Fatty acids usually contain between 14 and 22 carbon atoms, but fatty
acids with 16 and 18 carbon atoms are the most common (note that they
contain an even number of carbon atoms).
There are two major types of fatty acids:
1 those that have only carboncarbon single bonds (saturated fatty acids)
2 those that contain one or more carboncarbon double bonds
(unsaturated fatty acids). Monounsaturated fatty acids contain only
one C=C, whereas polyunsaturated fatty acids contain two or more
C=C. The C=C in fatty acids is almost always cis, and this results in a
bend (or kink) in the hydrocarbon chain (Figure B18).
Iodine number
It is possible to work out the degree of unsaturation, i.e. the number of
double bonds, within a fat or oil, using iodine. Iodine is able to add across
a double bond, as shown in Figure B19. As you can see, one molecule of
iodine reacts with one C=C, so the number of moles of iodine used up
in the reaction with a fat or oil can be equated to the number of double
bonds within the fat or oil molecule. For example, if two moles of iodine
reacted with one mole of fat or oil, then that would indicate that there
were two C=C within the fat or oil molecule.
HO
C
O
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH3
CH2
CH3(CH2)16COOH
stearic acid: saturated fatty acid
CH2
CH2
CH3
CH2
CH2 CH2
CH2
HO
C
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH3
CH2
CH2
HC
CH
CH
CH2
HC
CH
O
CH3(CH2)7CH=CH(CH2)7COOH
oleic acid: monounsaturated fatty acid
CH2
HO
C
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH
CH
HC
O
CH3(CH2CH=CH)3(CH2)7COOH
linolenic acid: polyunsaturated fatty acid
Figure B18 Examples of saturated and unsaturated fatty acids. All double bonds shown have cis geometry (see Chapter 10, page 489
in the Coursebook).
unsaturated fat
I2
addition product
Figure B19 The addition reaction between iodine and the double bond in an
unsaturated fatty acid.
A measure of the degree of unsaturation in a fat or oil may be given

by the iodine number. A saturated fat with wholly saturated fatty acids
will have an iodine number of zero, whereas an oil consisting of mostly
polyunsaturated fatty acids will have a high iodine number. For example,
if 65 g of iodine reacted with 50 g of fat or oil, then the iodine number
would be:
The iodine number is the number

of grams of iodine that reacts
with 100g of fat or oil.
65 2 = 130
(as the iodine number refers to the number of grams of iodine that reacts
with 100 g of fat/oil).
An iodine number of 130 would suggest that the oil contains a high
degree of polyunsaturated fatty acids such as linolenic acid (which has
three C=C). An animal fat, such as butter, which has a high degree of
saturated fatty acids, has an iodine number of between 25 and 45.
17
Worked example
Work out the iodine number, given the structural formula of linoleic acid:
Mr = 280.4 (Mr for I2 = 253.8)
CH3(CH2)4(CH=CHCH2)2(CH2)6COOH
To work out the iodine number of a known fatty acid, we must look at the number of double bonds in the fatty
acid.
Linoleic acid has two double bonds, and thus two moles of iodine (I2) will react with one mole of linoleic acid.
This means that 280.4 g of linoleic acid would react with 253.8 2, i.e. 507.6 g I2. 100 g of linoleic acid would
therefore react with:
100
507.6 = 181 g I2
280.4
Thus the iodine number for linoleic acid is 181.
Most triglycerides contain

a mixture of saturated,
monounsaturated and
polyunsaturated fatty acids:
those fats that are predominantly
made up of saturated fatty acids
are known as saturated fats;
those containing predominantly
monounsaturated fatty acids are
called monounsaturated fats (oils);
and those with predominantly
polyunsaturated fatty acids are
polyunsaturated fats (oils).
Fats and oils

The level of unsaturation in the fatty acids influences the melting point
of the fat or oil: triglycerides with a high proportion of saturated fatty
acids have higher melting points and are solid at room temperature, e.g.
animal fats such as lard and butter. This is due to the long hydrocarbon
chains being able to pack closely together, forming intermolecular
interactions (van der Waals forces).
Triglycerides rich in monounsaturated and polyunsaturated
fatty acids, on the other hand, have lower melting points and are oils at
room temperature (e.g. vegetable and fish oils). As we have already seen,
the C=C results in the formation of a bend within the hydrocarbon
chain. As a result, the hydrocarbon chains are not able to approach each
other as closely and form as many intermolecular interactions, hence
the lower melting point. As the number of C=C increases within the
triglycerides, they become more and more fluid, hence polyunsaturaterich triglycerides have lower melting points than monounsaturate-rich
ones, although both types are liquids at room temperature. It is customary
to call solid triglycerides fats and liquid triglycerides oils.
Omega-3 and omega-6 fatty acids
We would normally name a

carboxylic acid containing C=C
counting the C of the COOH
group as carbon 1. Omega is the
last letter of the Greek alphabet
and indicates that we are starting
from the end of the chain.
18
We obtain the majority of fatty acids that we need via our diet, although
we are able to synthesise most in the body. Two fatty acids which must
be obtained from the diet, as we do not possess the necessary enzymes to
biosynthesise them, however, are linoleic acid and linolenic acid these
are known as essential fatty acids, and dietary sources include linseed oil,
rapeseed oil and soybeans. Linolenic acid is also known as an omega-3
fatty acid, and linoleic acid as an omega-6 fatty acid. The omega refers to
the position of the first C=C, when the fatty acid is numbered starting
with the carbon at the opposite end to the carboxyl carbon (COOH
group) (Figure B20).
For example, linoleic acid has two C=C positioned at the sixth and
ninth carbons from the terminal CH3, but it is the first C=C that is
used to categorise it as an omega-6 fatty acid. Linolenic acid has three
O
C
HO
linoleic acid
4
5
2
1
omega-6 fatty acid
O
C
HO
linolenic acid
omega-3 fatty acid
1
2
Figure B20 Linoleic acid and linolenic acid, drawn without the bends in the
structures for clarity.
C=C: one C=C at the third carbon starting at the opposite end to the
carboxylic acid, the second at the sixth carbon, and the third at the ninth
carbon. It is thus an omega-3 fatty acid, as the first C=C is at carbon 3.
A diet rich in omega-3 fatty acids has been shown to have several
benefits on health. A regular intake of eicosapentaenoic acid (EPA)
(a longer-chain derivative of linolenic acid found in oily fish such as
salmon) and linolenic acid (found in flax seeds, soybeans and rapeseed
oil) can reduce the risk of heart attacks by lowering LDL-cholesterol (see
below) and triglyceride levels in the bloodstream. Omega-3 essential fatty
acids have also been associated with brain function and are sometimes
included in dietary supplements for pregnant women, to help boost brain
development in the growing fetus.
Trans fats
We have already seen that fats and oils can undergo addition reactions
across the C=C with iodine. Addition reactions may also be used in the
food industry, except this time using hydrogen to add across the C=C
double bonds in the unsaturated fatty acid, thus converting C=C double
bonds to CC single bonds. This results in what are called hydrogenated
fats, which have higher melting points, due to a higher degree of
saturation, and are therefore more solid at room temperature.
Hydrogenated fats were used in margarines and also in many processed
foods, as they prolong shelf-life (see Option F on the CD-ROM, page 7).
However, there is now a move to use alternatives to hydrogenated fats, as
they have been shown to have a negative effect on health. This is due to the
formation of trans fats during the hydrogenation process, in which trans
double bonds are formed in the fatty acid chain. Trans fats are associated
with an increase in the levels of LDL-cholesterol (see later) and thus an
increase in the risk of heart disease.
Digestion of fats
When fats are ingested, they must be broken down into smaller molecules
in order to be absorbed into the body from the intestines. This breakdown
is catalysed by enzymes (e.g. pancreatic lipase), which are secreted into
the intestines.
These enzymes catalyse the hydrolysis of the ester bonds in the
triglycerides into free fatty acids plus glycerol (propane-1,2,3-triol),
which are then absorbed (this is the reverse of the formation reaction
shown in Figure B17). Once absorbed, the fatty acids and glycerol are
reassembled into the triglycerides and transported to their destination.
19
Because they are hydrophobic (non-polar) molecules, they are poorly

soluble in the aqueous blood plasma and cannot be transported as free
molecules. Therefore they are transported via carriers called lipoproteins.
Lipoproteins play an important role in heart disease, and we shall talk
more about them when we look at the transport of lipids.
Phospholipids
The second major type of lipid in the body is the phospholipids.These
are the main lipids found in cell membranes. A membrane made up of a
bilayer of phospholipids surrounds each cell, and phospholipid membranes
also surround many of the inner structures (called organelles) within the cells.
Phospholipids are similar in structure to triglycerides, in that they
contain two fatty acid chains esterified (ester linkage) to two of the
alcohols of glycerol. However, they also contain a phosphate group,
which has reacted with the third alcohol of glycerol (phosphate ester
linkage). The phosphate also usually undergoes a condensation reaction
with an amino alcohol, for example, choline (Figure B21) to form a
second phosphateester linkage. A phospholipid bearing a choline alcohol
is called phosphatidyl choline (also known as lecithin). Phospholipids
therefore have a polar head (the phosphate ester) and a non-polar tail
(the two fatty acids). This property allows them to form bilayers when
placed in an aqueous environment, as they arrange themselves so that
CH3
H3C
choline
N+
CH3
CH2
CH2
O
phosphate
O
glycerol
H2C
HC
OC
polar head
CH2
non-polar
tails
fatty
acids
phospholipid
bilayer
phosphatidyl choline
Figure B21 Structure of phosphatidyl choline and a representation of the lipid bilayer.
20
the polar head groups are in contact with the water (to form hydrogen
bonds) while the non-polar tails minimise their exposure to the water and
interact with each other in the interior of the bilayer (Figure B21).
Steroids
The third main type of lipids in the body is the steroids. Examples include
cholesterol, the sex steroids (testosterone and oestrogen) and adrenal
hormones (hydrocortisone and aldosterone).
Steroids are hydrophobic (mostly non-polar) molecules, bearing a
common structure, known as the steroid backbone. This is made up
of three six-membered rings (called A, B and C) and a five-membered
ring (called D) fused together. The steroids vary depending on the type
and position of substituents on the steroid backbone. There is also usually
a carboncarbon double bond in either ring A or ring B. Oestrogens
are different to the other steroids, in that they have an aromatic A ring
(benzene ring).
Cholesterol (Figure B22) is a major steroid found in the body. It is
found in cell membranes, where it maintains fluidity of the membrane,
and it is also the precursor of other steroids, such as those mentioned
above, as well as bile acids and vitamin D. Although cholesterol plays an
important role in the body, it can also have a negative effect on health, in
that it can contribute to heart disease.
H3C
CH3 CH
CH3
CH2
CH2
CH2
CH
CH3
C
H3C
A
HO
cholesterol
B
steroid backbone
Figure B22 Structure of cholesterol and the steroid backbone.
Transport of lipids
Triglycerides and cholesterol are essentially insoluble in the aqueous
blood plasma and therefore cannot be transported as free molecules.
Therefore, these lipids assemble with phospholipids and proteins to
form particles known as lipoproteins. The inside of the lipoprotein is
hydrophobic, but the outside is hydrophilic and therefore can travel in the
bloodstream. There are different types of lipoprotein, classified according
to their relative densities. Each type has a different composition of protein,
triglycerides and cholesterol. Low-density lipoproteins (LDL) consist
mainly of cholesterol and are the major reservoir of cholesterol they
transport it throughout the body, where it can be stored in the tissues
or used (for example, in cell membranes). High levels of this LDLcholesterol can lead to fatty deposits in the walls of arteries in the heart
and elsewhere, leading to atherosclerosis (hardening of the arteries), which
can result in heart attack and stroke.
Another lipoprotein is high-density lipoprotein (HDL) this is a
protein-rich particle. It is smaller than LDL and denser, as it contains more
protein (protein is more dense than lipid). HDL consists of approximately
33% protein, compared with 25% protein for LDL. HDL scavenges
21
Low LDL-cholesterol levels and

high HDL-cholesterol levels
reduce the risk of heart disease.
cholesterol from LDL, tissues and artery walls and returns it to the liver,
where it is converted to bile acids. Thus, HDL removes cholesterol from the
tissues and arteries and has a beneficial effect with regards to heart disease.
LDL-cholesterol levels are not based on the amount of cholesterol
taken in the diet but rather on the amount and type of fat taken in.
Saturated fats (especially myristic, palmitic and lauric acids) and trans fats
increase the level of LDL-cholesterol in the body and are thus associated
with an increased risk of heart disease. Trans fats have also been found to
lower HDL-cholesterol levels.
Polyunsaturated and monounsaturated fats, however, have been shown
by some studies to lower LDL-cholesterol and increase HDL-cholesterol.
Therefore, the majority of fat taken in the diet should be in the form of
mono- and polyunsaturated fats, while intake of saturated fats and trans
fats should be limited (or totally excluded) in order to reduce LDLcholesterol levels.
Table B2 summarises the roles of the various lipids and gives some of
their positive or negative effects.
Type of lipid
Effects / roles
triglycerides
phospholipids
major component of cell membranes
steroids
cholesterol helps to maintain the uidity of cell membranes

and is a precursor for sex steroids, adrenal hormones, bile
acids and vitamin D
high LDL-cholesterol levels are associated with
atherosclerosis and heart disease
energy reserve
insulates and protects organs
insulates from heat loss through the skin
monounsaturated, polyunsaturated fatty acids and omega-3
fatty acids protect against heart disease by lowering LDLcholesterol
saturated fats such as lauric, myristic and palmitic acids
increase risk of heart disease by increasing LDL-cholesterol
high fat intake associated with obesity
Table B2 Functions and effects of the major groups of lipids.
Test yourself
10 Is the following fatty acid saturated or unsaturated? Would you expect a fat consisting mainly of this type of
fatty acid to be liquid or solid at room temperature?
O
C
HO
11 Is the following fatty acid an omega-3 or omega-6 fatty acid?

O
C
HO
12 The formulas of some fatty acids are shown below. Deduce the number of C=C in each and hence work
out the iodine number (Mr for I2 = 253.8).
C15H23COOH
C17H33COOH
C19H35COOH
C13H27COOH
13 A fatty acid with Mr = 254.46 has an iodine number of 100. Work out the number of C=C in the fatty acid.
22
B5 Micronutrients and macronutrients
Learning objectives
Nutrients are chemical substances derived from food that are used by
the body for growth and survival. We have so far discussed proteins,
carbohydrates and fats. All these are required in relatively large amounts
in the diet they are known as macronutrients, and other examples
include minerals such as sodium, magnesium, potassium, calcium,
phosphorus, sulfur and chlorine.
Macronutrients are chemical substances that are required in

relatively large amounts (>0.005% body weight) by the body.
Micronutrients, by contrast, are required in very small amounts by

the body (<0.005% body weight). Examples include vitamins and trace
minerals such as iron, copper, zinc, iodine, selenium, cobalt and manganese.
Their main functions are as co-factors for enzymes (a co-factor is a
non-protein component of an enzyme that is essential for its correct
functioning), but they may also be incorporated into certain hormones.
They are required in mg or g amounts, and some, if taken in high
amounts, can be toxic, e.g. the trace minerals.
Explain the difference between

micro- and macronutrients and
give examples.
Compare the structures of
vitamins A, C and D and relate
their structures to their relative
solubilities in water or fat
Deduce whether a vitamin is
water- or fat-soluble by looking
at its structure
Discuss the different types of
nutrient deficiencies around the
world, and the diseases they lead
to, and suggest ways of solving
the deficiency problems
Iodine is an important component of thyroid hormones.
Vitamins are micronutrients

Vitamins are organic molecules that are essential in small amounts for the
normal functioning of the body. There are two main classes of vitamins:
water-soluble vitamins and fat-soluble vitamins. Water-soluble vitamins
have structures that contain polar groups, for example OH groups, which
can hydrogen bond to water molecules. Examples include vitamin C (also
known as ascorbic acid) and the B group of vitamins (a group consisting
of eight different vitamins); these are readily excreted in the urine and
stores are rapidly depleted, so a regular daily intake is required.
Fat-soluble vitamins are mostly hydrophobic (non-polar) in nature,
consisting of long hydrocarbon chains or rings. Examples include vitamins
A, D, E and K. This type of vitamin is stored in the body, and therefore, if
excessive amounts are taken, levels can build up, resulting in toxicity.
Vitamin C (ascorbic acid)

This is a water-soluble vitamin, as it contains a number of hydroxyl
groups, which enable it to form hydrogen bonds with water (Figure
B23).Vitamin C plays a key role in tissue growth and repair more
specifically, it is required for the synthesis of collagen, a protein found in
connective tissue (for example, in bone, skin and blood vessels). It can also
act as an antioxidant, protecting the body from damage by free radicals
produced naturally during normal metabolic processes.Vitamin C is found
widely in fresh fruit and vegetables, particularly in citrus fruits. Deficiency
of vitamin C results in the disease called scurvy, symptoms of which
include swollen, bleeding gums, muscle and joint pain, and poor healing
of wounds.
H
H
HO
OH
H
C
H
HO
OH
Figure B23 Structure of ascorbic acid, a

water-soluble vitamin.
23
Vitamin A (retinol)
Vitamin A (Figure B24a) is a fat-soluble vitamin. It contains a long
hydrocarbon chain and a hydrocarbon ring, and although it does contain a
hydroxyl group, the polar nature of this group is not enough to offset the
non-polar nature of the rest of the molecule. Having mostly a non-polar
structure means that it is soluble in fat rather than water.
Vitamin A is important for vision, especially in low-light intensities; it
also plays a role in growth and development, skin repair and the immune
system.Vitamin A (in the form of retinol) is found in animal products, such
as liver, egg yolks and dairy products. It can also be formed in the body from
beta-carotene, a vitamin A precursor, found widely in fruit and vegetables
such as carrots. Deficiency of vitamin A results in a condition known as
xerophthalmia, a severe drying of the eye, accompanied by night blindness; it
is a leading cause of blindness in children in developing countries.
Vitamin D (cholecalciferol)
Examiners tip
You should be able to work
out from its structure whether
a particular vitamin is wateror fat-soluble.Vitamins
containing many OH
groups and/or several very
electronegative atoms (such as
N or O) are generally watersoluble, and those that consist
almost entirely of C and H are
fat-soluble.
Vitamin D is a steroid derivative; it is not a steroid, because it does

not have the characteristic steroid backbone (Figure B24b). It contains
one polar hydroxyl group and a large non-polar hydrocarbon backbone,
making it predominantly hydrophobic and therefore fat-soluble.Vitamin
D plays an important role in promoting the absorption of calcium
and phosphorus from food and in promoting mineralisation of bone;
it is present in butter, cheese, milk and fish liver oil.Vitamin D can be
synthesised in the body by the action of sunlight on pro-vitamins in the
skin, but deficiency can occur, for example in those with limited exposure
to sunlight, and also in children, who require larger levels of vitamin D for
growth.Vitamin D deficiency in children can lead to a condition called
rickets, characterised by softening and deformity of the bones.
H3C
CH3
H
C
CH3
C
CH
C
H
H
C
H3C
CH3
CH3
CH3
CH2OH
C
H
C
H
CH2
CH
H2C
CH2
HC
CH2
CH3
CH3
vitamin A (retinol)
HO
vitamin D (cholecalciferol)
Figure B24 Structures of the fat-soluble vitamins: (a) vitamin A; and (b) vitamin D.
Malnutrition
Malnutrition is the term used to describe an inadequate intake of
the nutrients needed to maintain good health. It can be caused by not
eating enough food and also from eating a poorly balanced diet: for
example, a diet of processed, fast foods, which lack necessary vitamins and
minerals. The problem of insufficient food intake is not just a problem
in the poorer developing countries: certain groups of the population in
industrialised countries are also at risk, for example, the elderly. Poorly
balanced diets are a growing problem in countries such as the USA and
the UK, where obesity levels are rising and diets rich in over-processed,
high-fat, low-nutrient foods, are increasingly common.
24
Micronutrient deciencies
Iron is a component of haemoglobin and is required for O2 transport.

A lack of iron in the diet leads to a reduced amount of haemoglobin
and red blood cells in the body, known as anaemia, symptoms of
which include feeling tired, breathlessness and palpitations. Iron
deficiency is thought to be the commonest micronutrient deficiency
in the world and occurs not just in developing countries but also
industrialised countries. Iron-supplementation of foods, such as
breakfast cereals, is one strategy to overcome this problem and has
proved to be successful in a number of countries.
Iodine in the diet is used to synthesise the thyroid hormone thyroxine,
which plays a major role in controlling the basal metabolic rate in adults
and growth and development in children. Deficiency of iodine results
in a condition called goitre (or goiter), characterised by a lump around
the throat area caused by an enlarged thyroid gland. Addition of iodine
to table salt has resulted in a substantial decrease in iodine deficiency.
Vitamin A deficiency can result in a condition called xerophthalmia,
which, as we have already mentioned, is a leading cause of blindness in
many developing countries. Fortification of foods with vitamin A has
proved a successful strategy at combating this deficiency. Fortification
of margarine has produced great success in many countries, but other
foods are also showing promise for example, sugar fortification (used
in Central America) and maize fortification (in Zimbabwe).
Vitamin B group: vitamin B3 (called niacin) is converted to a
coenzyme that plays a key role in oxidationreduction processes in the
cell. Deficiency results in a condition called pellagra, characterised by
diarrhoea, dermatitis and dementia.Vitamin B1 (thiamine) is converted
to a coenzyme that is necessary for energy production within the cell.
Deficiency leads to beriberi, characterised by muscle weakness. Many
foods, such as breakfast cereals, are fortified with niacin and thiamine,
and deficiency is rare in developed countries.
Vitamin C deficiency results in scurvy. Scurvy used to be a common
problem among sailors, who spent long periods at sea without fresh
fruit and vegetables, before it was recognised that a regular intake
of citrus and other fruits and vegetables would prevent this disease.
Nowadays, scurvy is rare in developed countries.
Vitamin D deficiency can result in rickets in children. As explained
above, it is a condition in which softening and deformity of the
bones occur due to a reduction in uptake of calcium and phosphate
from food. Fortification of dairy products with vitamin D means that
deficiency is now rare in industrialised countries. However, it is still a
problem in some developing countries, where intake of dairy products
may be low, or where religious or social customs and/or climatic
conditions prevent an adequate exposure to sunlight.
Selenium is important for the functioning of certain enzymes, which
mop up peroxides in the cell. Selenium is found in the soil and is taken
up by plants such as cereal crops; the milling process of the grain does
not remove the selenium, and thus it is usually taken in the diet in
sufficient quantity to prevent deficiency. However, in certain areas of
some countries, such as Russia and China, selenium levels in the soil are
too low, and in these cases selenium supplements are required.
25
Macronutrient deciencies
Protein
Protein deficiency is one of the most common forms of malnutrition in
developing countries and is associated with millions of deaths per year; it
is most common in young children at the time of weaning. There are two
types: marasmus and kwashiorkor. Marasmus is malnutrition caused by
an inadequate intake of both protein and energy, and is characterised by a
thin, emaciated appearance and stunted physical and mental development
if the condition persists. Kwashiorkor is malnutrition caused by an
inadequate intake of protein but an adequate energy intake; children
with this condition usually have a large belly, with stunted growth. These
conditions have a high death rate because they also result in a weakening
of the immune system, so that it is more difficult to fight infections; a
large number of children with protein deficiency in developing countries
die from infections rather than from the starvation itself.
Causes of deciencies
The types of nutritional deficiencies we have seen above are caused by:
food shortages in developing countries, due to lack of modern
agricultural methods, such as fertilisers and irrigation
poor food distribution and high food prices
chronic (long-term) illness, such as chronic infections, resulting in
decreased appetite, reduced ability to absorb nutrients, and excessive
excretion of nutrients due to chronic diarrhoea
poor diet due to lack of education or understanding of what constitutes
a balanced diet.
Some solutions
provision of energy- and nutrient-rich food rations

fortification of staple foods with micronutrients
genetic modification of food: for example, growing rice containing
beta-carotene to prevent vitamin A deficiency-related blindness in
children in developing countries
provision of nutritional supplements
help with implementation of modern agricultural methods in
developing countries
improving education with regards to how to eat a balanced diet.
Test yourself
14 Would you expect the following vitamin to be fat- or water-soluble?
O
26
B6 Hormones
Hormones are chemicals messengers they allow cells in the body to
communicate. They cause a specific effect on hormone-sensitive cells
(called target cells) in the body and the effect they cause depends on the
type of hormone and also the type of target cell. Hormones are produced
in glands known as endocrine glands (the study of the hormone system
is called endocrinology). The endocrine glands secrete the hormones
directly into the blood, where they then affect cells from other organs, or
from the organ from which they were released.
When the hormone reaches the target cell, it binds to a specific protein,
known as a receptor, either on the surface of the cell or inside the cell. It
is the binding of the hormone to the receptor that triggers the target cell
to produce a response.
There are many different types of hormone in the body; some are
proteins (e.g. insulin, antidiuretic hormone (ADH)), some are steroids (e.g.
oestrogen, testosterone, progesterone, aldosterone) and some are amino
acid derivatives (e.g. thyroxine, epinephrine).
Learning objectives
Describe how and where

hormones are produced and
explain their roles in the body
differences and similarities
of cholesterol and the sex
hormones
Outline how combined oral
contraceptives work to prevent
pregnancy
Describe the medical and nonmedical uses of steroids
Proteins and peptides as hormones

Insulin
The endocrine gland that produces insulin is the pancreas. Insulin is a
protein secreted into the bloodstream in response to high levels of glucose
in the blood. Insulin binds to insulin receptors on target cells to decrease
the amount of blood glucose by:
increasing the uptake of glucose in these cells (for example, muscle cells
and most other tissue cells) and increasing utilisation of glucose within
these cells, to produce energy
stimulating the liver to store glucose in the form of glycogen.
A common metabolic disease, known as diabetes mellitus, is caused by
either a deficiency of insulin or a reduction in the response of target cells
to insulin (known as insulin resistance). The effect is high levels of glucose
in the blood, which can lead to long-term complications such as nerve
damage, kidney failure, heart disease and stroke.
ADH
ADH is a short peptide produced in the pituitary gland in response to an
increase in osmotic pressure in the blood and also a reduction in plasma
volume (signs of dehydration). The main target cells of ADH are the
kidney tubules, which are made more permeable; there is an increase in
the uptake of water, resulting in more water being retained in the body
and less lost in the urine.
Steroid hormones
The steroid hormones include the corticosteroids and the sex steroids.
Aldosterone
Aldosterone is produced in the adrenal glands, in the adrenal cortex. It is
known as a corticosteroid and regulates the salt and water balance in the
body. It acts on the kidney tubules to increase the uptake of sodium and
water and to promote the loss of potassium.
27
Oestrogen and progesterone

Oestradiol is the most potent oestrogen (others are oestrone and oestriol).
It is produced in the ovaries in pre-menopausal women and has effects on
many types of cell in the body, for example, breast cells and endometrial
cells (lining the uterus). It is responsible for promoting female secondary
sexual characteristics, such as breast development, and also for regulating
the menstrual cycle (along with progesterone) and maintaining pregnancy.
Progesterone is also produced in the ovaries and prepares the body for
conception by preparing the endometrium for implantation of an egg.
If pregnancy occurs, it helps maintain pregnancy (during pregnancy, it is
produced in the placenta) and prepares the body for birth.
Testosterone
Testosterone is a male sex hormone (known as an androgen) produced in
the testes and has effects on many cells in the body. It is responsible for
promoting the male secondary sexual characteristics, such as deepening of
the voice, increase in muscle mass and strength, facial hair, etc.
Amino acid derivatives as hormones

Thyroxine
Thyroxine is an amino acid derivative containing iodine. It is produced
in the thyroid gland and has effects on all cells. It regulates metabolism,
controlling the amount of oxygen used up by cells. It is responsible for
generating body heat and for growth and development.
Hypothyroidism (in which the thyroid gland does not produce enough
thyroxine) is a common disorder, increasing with age, and results in a
slowing of metabolism, characterised by weight gain, tiredness and feeling
cold.
Epinephrine (adrenaline)
Epinephrine is secreted by the adrenal glands (in the medulla) and is a
major hormone of the part of the nervous system that prepares the body
for stressful situations. It acts on many cells of the body, for example, the
brain, muscles, blood vessels, heart, lungs and digestive system. It has many
effects, including: increasing blood pressure, and the strength and rate of
heart contractions, to pump more blood to the muscles; increasing the
breakdown of glycogen in the liver, to raise blood glucose levels so that
they can be utilised by cells; and dilating the vessels in the lungs so that
more oxygen can be supplied to the heart and muscles. All these effects
allow the body to deal with emergency situations, called the fight or
flight response.
Structure of steroid hormones

Steroid hormones all have a common structure, in that they all contain a
steroid backbone consisting of three six-membered rings and a fivemembered ring fused together. This was already touched on when we
talked about cholesterol. If we take cholesterol and the sex steroids as
examples, we can see that they all contain a steroid backbone, but they
differ in the type and position of substituents (functional groups) on
the steroid backbone (Figure B25). It is these differences that give the
particular steroid its biological properties.
28
H3C
CH3
CH
CH2
17
CH3
C
H2
H3C
CH2
CH
CH3
cholesterol
ketone
progesterone
HO
O
alkene
ketone
CH3
OH
O
alkene
OH
hydroxyl
benzene
ring
CH3
testosterone
alkene
CH3
hydroxyl
ketone
CH3
H3C
hydroxyl
CH3
oestradiol
HO
hydroxyl
Figure B25 Structures of cholesterol, progesterone, testosterone and oestradiol.
All contain a substituent at the C17 position, but in cholesterol it is

a branched hydrocarbon chain, whereas in progesterone it is a ketone
group, and in testosterone and oestradiol it is a hydroxyl group. Both
progesterone and testosterone have a ketone group at C3, whereas
oestradiol has a hydroxyl group (it is named thus as it contains two
hydroxyls and hence is a diol). Cholesterol has a C=C in the B ring (see
also Figure B22), whereas testosterone and progesterone have a C=C in
the A ring and oestradiol has an aromatic A ring (a benzene ring). It is not
surprising that all these steroids have similar structures, because oestradiol
is biosynthesised from testosterone, which is in turn biosynthesised from
progesterone, which is derived from cholesterol.
Oral contraceptives
There are different types of oral contraceptives probably the most
commonly used is called the combined oral contraceptive pill, which
contains a combination of oestrogen and progesterone. It works in
a number of ways: it prevents the release of an egg from the ovary,
i.e. it prevents ovulation from occurring; it makes the lining of the
endometrium thinner so that it is unsuitable for implantation of a
fertilised egg; and it makes the mucus in the cervix thicker to prevent
sperm from reaching the egg. If taken correctly, the combined oral
contraceptive pill can be more than 99% effective at preventing pregnancy.
Steroid use and abuse

As mentioned above, steroids are used medically as oral contraceptives.
They can also be used as hormone-replacement therapy (HRT) in women
who are going through the menopause. In the menopause, the ovaries
stop producing oestrogen, and so the level of oestrogen in the body drops
dramatically. This leads to symptoms such as night sweats, sleeplessness and
hot flushes. HRT replaces the hormones and thus alleviates the symptoms
of the menopause. Because HRT contains oestrogen, its long-term use has
been linked with an increase in the risk of breast cancer, as some types of
29
breast cancer are dependent on oestrogen for their growth. Once HRT is
stopped however, a womans risk of breast cancer starts to return to that of
the general population within three years of stopping treatment.
Other clinical uses of steroids include for the treatment of inflammation
and associated conditions. Hydrocortisone (also known as cortisol) is a
naturally occurring corticosteroid, so called because it is produced in
the adrenal cortex in the adrenal glands (there are two adrenal glands in
the body, one situated above each kidney). One of its effects is to reduce
inflammation, and therefore it, and synthetic corticosteroids, are used in
the clinic for a variety of conditions, such as eczema, rheumatoid arthritis
and asthma.
It was mentioned earlier that testosterone is an androgen (a male sex
hormone). It has uses medically as an androgen replacement in men who
have testosterone deficiency, for example, because of a disorder of the testes.
Androgens are also used non-medically, however for example, in sport.
Androgen abuse is the use of androgens for non-medical purposes
(they are called anabolic steroids because they promote tissue growth,
in particular of muscle). The three most common anabolic steroids that
are abused are testosterone and the synthetic derivatives nandrolone
and stanozolol. They are taken by sportsmen and women to enhance
performance, because they increase muscle mass and are also believed to
improve endurance. They have been used in disciplines such as athletics,
weightlifting and cycling. The ethical implications for taking anabolic
steroids is clear, in that it gives that person an unfair advantage over
their competitors and is thus cheating. It is a major concern to sporting
bodies worldwide, and random drug screening in major sporting events
is routinely employed to detect abuse. In the wider community, anabolic
steroids are also used for bodybuilding and by a minority of people in
certain occupations, such as security guards and bouncers, for cosmetic
reasons to give themselves a more masculine and intimidating look.
Abusing anabolic steroids can have a major impact on the body their
use can cause a number of side effects, such as breast growth in men,
acne, infertility, mood swings and aggressiveness. They can also cause high
blood pressure, liver disease (including cancer), heart attack or stroke.
Psychologically, abusers of anabolic steroids can become addicted to them,
developing an increased desire to keep taking them, even if unwanted side
effects occur.
Test yourself
15 Label the rings A, B, C
and D and state how many
ketone groups are present
in this steroid.
H3C
CH3 C
CH3
30
B7 Enzymes
Enzymes are proteins evolved by living organisms for the specific function
of catalysing biochemical reactions. They are found throughout the
cell and catalyse virtually every conversion that occurs in the cell. Some
enzymes are also found outside the cell for example, in the blood plasma.
There are many types of enzyme, and each type has a name based on the
type of reaction it catalyses and/or on the type of molecule on which
it acts. For example, transferase enzymes catalyse transfer of a functional
group, oxidoreductase enzymes catalyse oxidationreduction reactions,
proteases break down proteins and lipases break down lipids. Note that the
enzyme name ends in -ase; this is true for most enzymes.
Enzymes are proteins, and their activity is dependent on their
shape, i.e. their tertiary structure. A number of enzymes also
have a quaternary structure, where they consist of two or more
sub-units. Thus, quaternary structure is also important for the
functioning of those enzymes.
Enzymes act as biological catalysts they speed up biochemical reactions
in the body without themselves undergoing any permanent chemical
change. Most reactions catalysed by enzymes would not proceed to any
significant extent without the presence of enzymes enzyme-catalysed
reactions are typically 108 to 1012 times faster than the corresponding
uncatalysed reactions. They speed up reactions by lowering the
activation energy of the reaction; they do not make an unfavourable
reaction favourable (see Chapter 6, page 250 of the Coursebook). They
do this by providing an alternative pathway for the reaction, which has a
lower activation energy. They also provide an area (the active site) for the
reactants to come together and thus make it more likely that the reactants
will react.
The reactants involved in enzyme-catalysed reactions are called
substrates, and enzymes are highly specific for the particular substrate
on which they act. Some enzymes act on only one substrate, whereas
others act on a group of related substrates.
The enzyme must bind temporarily to the substrate for the reaction to
take place. This binding takes place in a mostly hydrophobic pocket called
the active site. The active site is normally situated near the surface of the
enzyme, towards one end of the protein. The active site is where catalysis
takes place, and its shape is key to the specificity of the enzyme.
The type and position of amino acids in the active site make it specific for
substrates of a certain size and shape.
When a substrate (S) binds to the enzyme (E) active site, it forms a
reaction intermediate known as an enzymesubstrate complex (ES).
This is when the substrate enters the active site and forms interactions
with R groups of amino acids in the active site. The type of binding
is reversible, i.e. weak bonding such as hydrogen bonds, electrostatic
interactions and van der Waals forces.
Formation of the enzymesubstrate complex can cause the substrate
molecule to become strained (distorted), and this will then more readily
form the product (P), with regeneration of the enzyme. The product then
diffuses away from the enzyme active site, as it does not bind as effectively
HL
Learning objectives
Describe the structure and

function of enzymes as
biological catalysts, including
the mechanism of enzyme
action, and proposed models for
substrate binding
Describe how enzyme
activity changes with substrate
concentration
Determine Vmax and the
Michaelis constant (Km) by
graphical means and explain the
importance of Km
Explain how heavy metal ions,
temperature changes and pH
changes can affect enzyme
activity
Compare the modes of action
of competitive and noncompetitive inhibitors, including
how they affect Vmax and Km
Describe the similarities and
differences between enzymes
and inorganic catalysts
31
HL to the active site as the substrate. A general equation for the reaction is
given below:
E+S
ES E + P
Enzyme specificity was first compared to a key (the substrate) fitting into
a lock (the active site of the enzyme). This was called the lock-and-key
hypothesis and it proposed that the active site was a complementary
shape to the substrate, like a specific key is a complementary shape to its
lock (Figure B26). However, a more recent hypothesis proposes that for
some enzymes, when the substrate enters the active site, it can cause a
change in the shape of the active site to better accommodate the substrate,
i.e. the active site changes to a shape complementary to the substrate
only after the substrate has entered the active site. This is known as the
induced-fit hypothesis (Figure B27).
enzyme
active site
enzymesubstrate
complex
substrate
Figure B26 The lock-and-key hypothesis.
enzyme
substrate
complex
enzyme
active site
substrate
enzyme active
site changes shape
slightly to accomodate
substrate
Figure B27 The induced-t hypothesis.
Enzyme kinetics
A lot of work was carried out at the beginning of the 20th century to
study the effects of substrate concentration on enzyme activity. At low
substrate concentrations, the rate of the enzyme-catalysed reaction is
proportional to the substrate concentration. As the substrate concentration
increases, however, the rate of reaction increases, but to a lesser extent,
and is no longer proportional to substrate concentration. Then at high
substrate concentrations, the rate of reaction remains constant and does
not increase further with an increase in substrate concentration.
This can be explained as follows: when the substrate is in low
concentration, there is a sufficient number of enzyme active sites
available to bind substrate and form the ES complex, so as the substrate
32
concentration increases, more ES forms and the rate increases proportional HL

to the increase in substrate concentration. The rate is essentially first order
with respect to the substrate.
As the substrate concentration increases further, however, some of the
active sites are already occupied with substrate and so there are not enough
active sites to bind all of the substrate.This means that the rate of reaction
increases less than would be expected when the substrate concentration
increases.This results in a slowing down in the increase of the rate of reaction
and the rate is now no longer proportional to the substrate concentration.
When the substrate concentration is high, all of the active sites of the
enzyme molecules are occupied by substrate, and so the rate of reaction
remains constant (maximum rate), i.e. any further increase in substrate
concentration results in no increase in rate of reaction, as the enzyme is
saturated with substrate. The enzyme is working at maximum capacity
as soon as an active site becomes vacant, it is occupied almost immediately
by a substrate molecule. The rate is zero order with respect to the substrate
when the substrate concentration is sufficiently high.
The curve produced is known as a MichaelisMenten curve (Figure
B28), named after Leonor Michaelis and Maud Menten, who were
pioneers in enzyme kinetics. Note from the curve that the rate for an
enzyme saturated with substrate is known as the maximum velocity
(Vmax). Vmax varies from one enzyme to another and is dependent on
reaction conditions such as temperature and pH.
Note also the Michaelis constant (Km). This is the concentration
of substrate when the rate is equal to one half Vmax. Km is a
useful constant, as it gives an indication of the affinity of an enzyme
for a substrate, i.e. how well the enzyme binds the substrate (it is thus
a measure of the stability of the ES complex). If an enzyme has a low
Km, this indicates that it has a high affinity for a substrate, as only a small
concentration of substrate is needed for the reaction to proceed at half
its maximum velocity. Large Km values indicate that the enzyme has less
affinity for the substrate, as a large concentration of substrate is needed to
reach half Vmax.
Vmax
Rate of reaction
maximum velocity
for the reaction
1
2 Vmax
Km
Concentration of substrate
Figure B28 The MichaelisMenten curve.
33
HL
Factors that inuence enzyme activity

Enzymes have evolved to work optimally under the conditions to which
they are exposed in the body. If these conditions are changed significantly,
this can have a dramatic effect on the functioning of the enzyme. Three
factors that can influence enzyme activity are temperature, pH and the
presence of heavy metal ions.
Temperature
Temperature has an effect on enzymatic reactions (Figure B29): as the
temperature increases, the kinetic energy of the system increases and there
is more chance that substrates with energy greater than the activation
energy will collide with the enzyme active site. Also, as the temperature
increases, more collisions occur in a certain time between the enzyme and
substrates. Therefore, increasing the temperature increases enzyme activity.
Rate of reaction
optimum
temperature
denaturation
occurs, leading
to loss of enzyme
activity
20
40
Temperature / C
60
Figure B29 The effect of temperature on enzyme activity.
This is true only up to a certain point if the temperature increases

too much, the rate of the enzymatic reaction will decrease. This is because
at higher temperatures, the kinetic energy (vibrations) of the enzyme
will break the interactions that hold the enzyme, and thus the active site,
in its specific three-dimensional shape. As the shape of the active site
is key to the activity of the enzyme, any change in shape will result in
loss of functioning of that enzyme, as it will no longer be able to bind
the substrate effectively. The loss of the tertiary structure is known as
denaturing.
pH
Enzymes work within a relatively narrow pH range, depending on the pH
of their environment in the body. The optimum pH varies widely from
one enzyme to another: for example, digestive enzymes such as pepsin,
which act in the stomach, have an optimum pH of approximately 1.5
to 2.5, which is the pH that they would be exposed to in the stomach;
however, digestive enzymes that act in the intestines, such as pancreatic
lipase, have an optimum pH of approximately 8.
34
If the enzyme is exposed to a pH above or below its optimum pH,

HL
activity starts to decline. This is for two reasons: firstly, some enzymes
contain ionisable amino acids at the active site that participate in the
catalytic action of the enzyme; changes in the pH affect the ionisation
of those amino acids and thus influence their ability to participate in the
reaction.
A second reason for the decline seen in enzyme activity is denaturation:
significant changes in pH change the charges on the R groups of the
amino acids that form the intramolecular interactions that dictate the
shape of the active site. The resultant change in shape results in a loss of
function of that enzyme, as described above for temperature.
The optimum temperature

for enzymes in the human
body is around 37 C, i.e.
body temperature. Above that
temperature, the enzyme starts to
denature as bonds responsible for
holding the protein in its threedimensional shape break.
The presence of heavy metal ions

Heavy metals such as silver (Ag+), mercury (Hg2+) and lead (Pb2+) have
strong affinity for sulfhydryl (SH) groups they react with sulfur atoms of
the sulfhydryl groups found in cysteine residues in the enzyme active site,
replacing the hydrogen atom. The shape of the enzyme is thus altered if
these cysteine residues are involved in forming interactions that contribute
to the tertiary structure of the enzyme, as they are no longer able to do so.
This is the mechanism by which these heavy metals are poisonous.
Enzyme inhibitors
If a chemical binds to an enzyme and prevents it from carrying out its
catalytic activity, the enzyme is said to be inhibited, and the chemical
is called an enzyme inhibitor. There are two main types of enzyme
inhibitors, depending on where they interact with the enzyme:
competitive inhibitors and non-competitive inhibitors. Enzyme inhibitors
are widely used as medicinal drugs, the most common being the
competitive inhibitors.
Competitive enzyme inhibitors

As their name suggests, competitive inhibitors compete with the natural
substrate for binding to the enzyme they thus bind to the active site
of the enzyme. Competitive inhibitors normally have a structure similar to
the natural substrate this allows them to form interactions with the active
site. Once the inhibitor enters the active site, it binds, forming an enzyme
inhibitor complex (rather than an enzymesubstrate complex). The
inhibitor is not acted on by the enzyme and so does not form products
instead, it blocks the entry of the substrate and thus stops the enzyme from
acting on the substrate and carrying out catalysis (Figure B30).
enzyme
active site
competitive
inhibitor
competitive inhibitor
binds to active site and
stops substrate bonding
substrate
Figure B30 The mechanism of a competitive inhibitor.
35
HL
Competitive inhibitors are usually reversible, so the enzymeinhibitor

complex breaks down to release the inhibitor, which then leaves the active
site. Because the inhibitor and substrate are competing for the active site,
increasing the substrate concentration will make it more likely that the
substrate will enter the active site, and thus inhibition will be reduced. The
maximum velocity (Vmax) of the reaction will remain the same, but it will
take a higher concentration of substrate to reach Vmax, so the Km will be
higher (Figure B31).
Vmax
Rate of reaction
no inhibitor
present
competitive
inhibitor present
1
2 Vmax
Km
Km
Substrate concentration
Figure B31 The effect of a competitive inhibitor on Vmax and Km.
Non-competitive inhibitors
Non-competitive inhibitors do not compete with the natural substrate, as
they do not bind to the active site, but another region of the enzyme. This
binding causes a conformational change in the shape of the active site,
which prevents the substrate from binding (Figure B32). As the inhibitor
does not compete with the substrate for the same site, increasing the
substrate concentration does not reduce inhibition. This means that the
Vmax is reduced in the presence of this type of inhibitor, but the Km is the
same (Figure B33).
noncompetitive
inhibitor
binding of
inhibitor
active
site
substrate
shape of active site

changed so that
substrate cannot bind
Figure B32 The mechanism of a non-competitive inhibitor.
36
HL
Vmax
Rate of reaction
no inhibitor
present
Vmax
non-competitive
inhibitor present
1
2 Vmax
1
2 Vmax
Km
Substrate concentration
Figure B33 The effect of a non-competitive inhibitor on Vmax and Km.
How do biological catalysts compare with

inorganic catalysts?
Both enzymes and inorganic catalysts speed up reactions by providing

an alternative pathway of lower activation energy. Neither changes the
position of equilibrium or yield of the reaction.
Enzymes are highly specific for their substrate, whereas inorganic
catalysts are often non-specific and can catalyse several reactions.
Enzymes have an optimum temperature and are denatured at high
temperatures, whereas inorganic catalysts are much less affected by the
conditions and generally work well at high temperatures.
Enzymes display saturation kinetics, i.e. reach a maximum velocity
when substrate concentration is increased; most inorganic catalysts
generally do not show saturation.
Test yourself
16 Enzyme X has a Km of 2.0 107 mol dm3 for a particular
substrate, whereas enzyme Y has a Km of 2.0 106 mol dm3
for the same substrate. Which enzyme binds better to the
substrate?
17 What types of interactions are possible between a competitive
reversible inhibitor and the enzyme active site?
37
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Learning objectives
Describe the structures of

nucleotides and polynucleotides
(nucleic acids)
Describe the differences in
structure between DNA and
RNA
Explain the double helical
structure of DNA
Describe how DNA carries the
genetic code, and explain how
DNA directs protein synthesis
Describe the steps involved in
DNA profiling and explain its
role in criminal investigations
and in paternity cases
O
O
phosphate
5'
CH2
4'
H
base
O
H
2'
H
3'
OH
pentose
sugar
B8 Nucleic acids
As their names suggest, deoxyribonucleic acid (DNA) and ribonucleic
acid (RNA) are nucleic acids. DNA carries the genetic code of the
organism. When cells divide (make copies of themselves), the DNA of the
cell must be copied (called DNA replication) so that the new cells will
have the same set of genetic information within them. When organisms
reproduce, they copy their DNA and pass it on to the next generation. All
organisms house their genetic information within DNA, except for some
viruses, which use RNA.
Structure of nucleic acids

Nucleic acids are polymers made up of monomers known as nucleotides.
Nucleic acids are thus also called polynucleotides.
Nucleotides consist of a five-carbon (pentose) sugar, an organic
nitrogen-containing heterocycle (N is part of the ring) called a base and a
phosphate group (Figure B34).
The pentose sugar is different in DNA and RNA. In RNA, the sugar is
ribose, and in DNA, the sugar is 2-deoxyribose, as it lacks an oxygen at
the C2 position (Figure B35).
HO
5'
CH2
O
H
1'
H
OH
H
2'
OH
OH
HO
5'
CH2
1'
H
ribose
OH
O
H
H
OH
H
2'
H
1'
H
2-deoxyribose
Figure B35 Structures of ribose and deoxyribose.
Figure B34 The general structure of a

nucleotide.
Note that we use the numbering

C1 to C5 ( = prime) when
talking about the sugar carbons
in a nucleotide. This is because
in nucleotides, the atoms of the
base are numbered 1 to 6 (in
pyrimidines) or 1 to 9 (in purines),
and so to avoid confusion, the
carbon atoms in the sugar are
numbered C1 to C5.
38
The bases of nucleic acids are derivatives of either purine or

pyrimidine (Figure B36) and are known as purines and pyrimidines.
The purines that occur in nucleic acids are adenine (A) and guanine
(G); the pyrimidines are cytosine (C), thymine (T, in DNA not RNA)
and uracil (U, in RNA not DNA) (Figure B36). The base is bonded
to the sugar at the C1' position of the sugar. The phosphate group in a
nucleotide is usually attached to the oxygen of the C5' hydroxyl group of
the pentose sugar.
Nucleotides join together to form polynucleotides. The type of reaction
is a condensation reaction between the phosphate attached to the C5'
of one nucleotide and the hydroxyl group at C3' of another nucleotide.
The nucleotides are thus joined covalently by a phosphodiester link
(phosphate ester on both sides) between the sugars (Figure B37). Nucleic
acids may consist of thousands of nucleotides linked together.
RNA is a single strand of nucleotides, whereas DNA is a double
strand. Each strand of nucleotides has a repeating sugarphosphatesugar
phosphate backbone, and attached to each sugar is a base.
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N
N
H
purine
pyrimidine
NH2
N
O
N
N
H
NH
N
H
purine
bases
NH2
N
guanine (G)
adenine (A)
NH2
H3C
NH
N
H
Examiners tip
You are not required to learn
the structures of the nucleotide
bases, but you should be able
to recognise them.
N
H
cytosine (C)
pyrimidine
bases
NH
O
N
H
thymine (T)
uracil (U)
Figure B36 The structures of purines and pyrimidines found in DNA and RNA.
O
N
NH
N
CH2
H
O
NH2
H
O
CH2
H
O
O
(C)
phosphodiester
link
NH2
(G)
3'
O
P
NH2
H
H
N
(A)
5'
CH2
H
H
3'
O
P
1'
O
Figure B37 Nucleotides joined by a phosphodiester link in a strand of DNA.
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Differences between RNA and DNA

The differences between DNA and RNA are summarised as follows:
DNA is a double-stranded nucleic acid, whereas RNA is single
stranded
DNA contains thymine, whereas RNA contains uracil as a base
DNA contains deoxyribose (no OH on C2') as the sugar, whereas
RNA contains ribose.
Structure of DNA
Watson and Crick famously proposed the double-stranded structure of
DNA in 1953. DNA is a double helix, consisting of two polynucleotide
strands that spiral around an axis. Each complete turn of the helix is ten
nucleotides in length. The sugar-phosphate backbone in each strand
winds around the outside of the helix, with the nucleotide bases attached
to the sugars stacked in the interior of the helix. The hydrophilic sugarphosphate backbone is thus exposed to the aqueous environment of
the cell, while the relatively hydrophobic bases are shielded from this
environment in the interior of the helix.
Each of the bases on one strand forms hydrogen bonds with a
base on the opposite strand. The bases pair together in a specific way:
the adenine bases on one strand form hydrogen bonds only with the
thymine bases on the opposite strand (two hydrogen bonds) and the
guanine bases on one strand hydrogen bond only with cytosine bases
on the other strand (three hydrogen bonds). This specific interacting of
bases is known as base pairing, and the two bases involved are called base
pairs (Figure B38). Each base pair consists of one purine base and one
pyrimidine base.
The structure of DNA has been likened to a ladder, which has been
twisted into a helix. The base pairs are the rungs of the ladder, whereas the
sugar-phosphate backbones are the sides of the ladder (Figure B39).
DNA carries the genetic code

The nucleus of the cell houses the chromosomes; in humans, there are
46 chromosomes per nucleus, made up two sets of 23 chromosomes, one
set inherited from each parent. Chromosomes are long, coiled strands of
DNA and proteins. The DNA in these chromosomes contains genes,
which carry all the information needed for the individual to grow, live
and reproduce.
Genes are stretches of nucleotides in the DNA. Each gene has a
specific sequence of nucleotides. As the sugars and the phosphates
within DNA are constant, it is the sequence of nucleotide bases
that gives each gene its originality.
When a cell divides, it needs to copy its DNA so that the new cell
will have an identical set of chromosomes to the parent cell. The process
of copying DNA is called DNA replication and involves unwinding
and separating the two strands of DNA, accompanied by breaking the
hydrogen bonds between the base pairs. This exposes the nucleotide bases
of the DNA (which were in the interior of the helix) and allows the bases
40
base pairs
H
H
O
N
O
CH2
O
O
CH2
O
3'
O
O
H
O
H2C
H3C
H
(T)
O
P
O
(A)
H
CH2
(G)
(C)
H
H
H
O
N
H
H2C
(C)
(G)
O
H
H
O
H2C
O
DNA
strand
HL
N
hydrogen
bonds
O
DNA
strand
Figure B38 Complementary base pairing in DNA.
on each of the DNA strands to be used as a template for the formation of

a complementary DNA strand (Figure B40).
The formation of the new strands occurs by free nucleotides forming
complementary base pairs with the DNA template strands: guanine
nucleotides pair with cytosine bases on the DNA strand; thymine
nucleotides pair with adenine bases on the DNA strand, and so on. The
free nucleotides are joined together by phosphodiester links to form the
new strands of DNA.
So how do genes carry the code for life? To understand this, we need
to know that each gene carries the code for the production of a single
41
parent
strand
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parent
strand
C
A
C
T
C
G
A
A
C
A
G
C
T
Remember that proteins are

made up of a specific sequence
of amino acids (called the
primary structure). This sequence
gives the protein its shape and
therefore its function, and it is
the sequence of nucleotide
bases within each gene that
dictates the primary structure
of the protein produced. In
other words, the information
for the structure of each protein
is carried in the sequence of
nucleotide bases within the
particular gene.
Translation is the process of

protein synthesis in which the
code held in the sequence of
bases of the mRNA is translated
into the sequence of amino acids
(primary structure) of the protein.
T A
DNA strands
separate
A
C
T
G
T
C
A
G
A
G
T
C
T
C
hydrogen
bonds
C
G
G
A
G
Figure B39 The double-helix structure

of DNA.
T
G
C
C
G
G
A
G
T
C
A
42
G
T
T
C
free nucleotides
base-pair with
bases on the parent
DNA strand and
are joined to the
growing DNA daughter
strand
A pairs with T
G pairs with C
A
G
newly synthesised
daughter strands
Figure B40 DNA replication.
protein. It is these proteins produced by the cell that carry out the
thousands of biochemical processes that are responsible for life.
For a cell to produce a protein, the gene must first undergo a process
called transcription. This occurs in the nucleus, and the first step in this
process is the unwinding and separation of the two strands of DNA on
which the gene is situated. In a similar manner to DNA replication, this
exposes the nucleotide bases of the gene and allows the bases on one of
the DNA strands to be used as a template.
Transcription differs to DNA replication, however, in that only one
strand of DNA is used as a template and the complementary strand
produced is a ribonucleic acid called messenger RNA (mRNA). The
complementary strand of mRNA is built up through complementary
RNA nucleotides (called ribonucleotides) forming base pairs with
the exposed bases of the DNA template. Guanine pairs with cytosine
and adenine pairs with uracil (not thymine, as in DNA). As each
ribonucleotide comes in and forms a base pair, it is joined covalently to
the growing mRNA chain by a phosphodiester link. This results in the
production of a strand of mRNA that has the complementary sequence
of bases to the gene of the DNA template strand. This mRNA then leaves
the nucleus and enters the cytoplasm, where it takes part in the second
process to produce a protein, known as translation.
During translation, the mRNA first attaches to a ribosome (a small

HL
organelle in the cytoplasm) and the code is read by a type of RNA called
transfer RNA (tRNA). tRNAs are small RNA molecules with an amino
acid covalently attached to one region of the molecule. Another region
of the same tRNA molecule interacts with complementary bases on the
mRNA. The tRNA interacts with a sequence of three nucleotide bases
on the mRNA; these three bases are called a triplet code, or codon, and
the three complementary bases on the tRNA are called an anticodon.
Each codon corresponds to only one amino acid, although several
codons may correspond to the same amino acid. For example, the
codon UUU on mRNA corresponds to the amino acid phenylalanine.
By this, we mean that a tRNA molecule with the anticodon AAA
(remember A base pairs with U) will have a phenylalanine amino acid
covalently attached to it. The anticodon of tRNA will interact with the
complementary codon on the mRNA and the phenylalanine amino acid
will get incorporated into the growing polypeptide chain. The mRNA
is read sequentially, so the next three bases (codon) will be exposed in
the ribosome and then the complementary tRNA molecule bearing its
specific amino acid will interact with it, incorporating the amino acid into
the polypeptide chain. And so on, and so on (Figure B41). Thus we can
now see how the sequence of bases in the DNA dictates the sequence of
amino acids in the protein synthesised.
DNA proling
DNA profiling is a method used to identify individuals by differences
in their DNA. It is used to identify criminals or exonerate suspects in
criminal cases, as well as to determine whether certain people are related,
for example in paternity cases, where there is a dispute over who is the
father of a child.
DNA profiling does not look at the whole of an individuals DNA,
as only a small percentage of the DNA varies between individuals. The
method looks at regions of the DNA that show high variability among
individuals. These are non-coding regions of DNA: stretches of nucleotide
bases that do not code for any protein. In these non-coding regions are
areas known as short tandem repeats (STRs), which are nucleotide
base-pair sequences (of about three to five base pairs in length) that repeat
over and over again in a region (known as a locus) of the chromosome
(e.g. ACTACTACTACTACTACT). The number of times this sequence of
bases (ACT in this case) repeats varies between individuals. DNA profiling
analyses samples of DNA from a number of loci on the chromosomes
(usually ten STR samples from ten different chromosomes). This builds
up a DNA profile for that individual. Statistically, no two people are likely
to have the same number of repeats in all of the STRs looked at (except
identical twins), and hence this profile is as unique as a fingerprint. DNA
profiling is commonly known as DNA fingerprinting.
The procedure first involves isolation of the DNA from the sample
source. In the case of DNA profiling in forensic cases, the source can be
blood, semen, skin cells, hair or saliva (e.g. from a cigarette butt) found at
the scene of a crime, or it can be a blood sample taken from a suspect (to
compare the DNA).
amino
acid
tRNA
mRNA
b
Figure B41 The process of translation. (a)

Two tRNA molecules interacting with the
codons on the mRNA. When the second
tRNA molecule (bearing the blue amino
acid) comes in and interacts with the mRNA,
the growing polypeptide chain is cleaved
from the rst tRNA molecule and joined
to the amino acid on the second tRNA
molecule. (b) The rst tRNA molecule then
leaves and a new tRNA molecule will come
in and interact with the next codon on the
mRNA chain. The polypeptide chain will then
be joined to the amino acid on this new
tRNA molecule, and so on, and so on, until
the complete polypeptide chain has been
produced.
43
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Figure B42 A DNA prole.
The isolated DNA is cut into small pieces using restriction enzymes
that recognise specific base sequences in the STR regions of the DNA.
These enzymes act like a pair of scissors, chopping up the DNA at those
particular sequences. Multiple copies of these STR regions are then
produced using a technique known as polymerase chain reaction
(PCR). PCR uses a DNA primer (to initiate DNA replication) and a
DNA polymerase enzyme (to polymerise nucleotides to produce new
complementary strands of DNA). In this way, thousands or millions of
copies of the DNA fragments may be produced.
These DNA fragments are then separated according to size using gel
electrophoresis. DNA bears a negative charge (owing to the phosphate
groups), and DNA fragments thus move towards the positive electrode
when an electric field is applied. Smaller fragments move faster than larger
fragments, and thus move further down the gel sheet.
The resulting pattern of bands is then transferred to a nylon membrane,
and a radioactive label such as 32P is then added, which combines with
particular bands of the DNA. X-ray film is then exposed to the radiation
produced by the 32P and developed the DNA fragments appear as dark
bands on the film (Figure B42). The pattern of the bands is unique to a
particular individual, and so this pattern is compared to the DNA patterns
of the suspect(s) to see if there is a match.
DNA profiling can also be used in paternity cases, where the DNA
patterns are compared to see if there are significant matches between
child and proposed father. Half of the childs genetic material is from
the father, so half of the DNA fragment bands of the child should
match those of the father (the other half should match those of the
mother).
Test yourself
18 Name the only nucleotide base that does not contain an amide
functional group.
19 Which nucleotide base complementary base pairs with guanine
and how many hydrogen bonds form between the two bases?
Learning objectives
44
Compare the processes

of aerobic and anaerobic
respiration, highlighting the
redox reactions involved and the
energy released
Describe the role of copper
ions (in cytochromes) in
electron transport and iron ions
(in haemoglobin) in oxygen
transport
B9 Cellular respiration
Organisms need energy to carry out the thousands of biochemical
processes that maintain life. Humans derive their energy from food:
glucose from carbohydrate and fatty acids from fats, for example, are
broken down in the cell in a series of reactions that yield energy in the
form of a molecule called ATP. This ATP is then used to fuel cellular
reactions, such as protein synthesis, and many other enzyme-catalysed
processes that occur in the cell.
There are two ways that these food molecules can generate energy,
called aerobic and anaerobic respiration. Aerobic respiration results in the
production of more ATP than anaerobic respiration and thus yields more
energy.
Aerobic respiration involves oxygen. Therefore it is carried out
when oxygen is present. The process involves the oxidation of food
molecules, such as glucose, to produce carbon dioxide, water and energy

(in the form of ATP).
General equation:
HL
C6H12O6 + 6O2 6CO2 + 6H2O + energy

The first step in the breakdown of glucose is common to both aerobic
and anaerobic respiration and involves a series of reactions known as
glycolysis.
Glycolysis
Glycolysis involves the breakdown of the six-carbon sugar glucose to
two three-carbon molecules called pyruvate. This process occurs in the
cytosol (intracellular fluid) of the cell and does not require oxygen. There
are ten enzyme-catalysed steps involved in the production of pyruvate, but
the overall reaction can be simplified:
H3C
C6H12O6
O
C
glucose
pyruvate
During glycolysis, the glucose molecule undergoes oxidation (loss

of electrons) to yield pyruvate (the average oxidation number of C in
glucose is 0 but it is +23 in pyruvate); the coenzyme nicotinamide adenine
dinucleotide (NAD+) gets reduced to NADH in the process.
The process of glycolysis uses up two molecules of ATP for every
glucose molecule converted to pyruvate; however, four molecules of ATP
are generated, so there is a net production of two ATP molecules.
The fate of pyruvate is different depending on whether oxygen is
present or not. Under anaerobic conditions (where oxygen is not
available), the pyruvate is reduced. In humans, for example in muscle
cells during exercise, oxygen becomes in short supply and there is not
enough to keep up with the demands of the cell; in this case, the pyruvate
is reduced to lactate (the average oxidation number of C in lactate is 0).
NADH is oxidised in the process to NAD+.
A coenzyme is an organic
molecule needed by an enzyme to
be fully active.
The average oxidation number of

C is worked out by assuming that
O has an oxidation number of 2
and H of +1.
H
H
H
O
C
O
C
+ NADH + H
pyruvate
O
C
+ NAD+
O
lactate
O
C
+ H+
O
In microorganisms such as yeast, anaerobic conditions resultHin pyruvate
being reduced to ethanol (average oxidation number of C is 2
in
pyruvate
ethanol) and carbon dioxide. This occurs in two stages:
H + CO2
H
ethanal
O
C
+ H+
O
H
pyruvate
H + CO2
H
ethanal
ethanal

H
+ NADH + H+
H + NAD+
ethanol
45
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This is the basis of fermentation and the overall reaction starting from
glucose is:
C6H12O6 2C2H5OH + 2CO2
glucose
A brief, simplified summary of

aerobic respiration.
1 Glucose is converted to two
molecules of pyruvate during
glycolysis.
2 Pyruvate undergoes a series of
reactions, including entry into
the citric acid (Krebs) cycle
and is oxidised to CO2. During
the oxidation steps, NAD+
becomes reduced to NADH.
3 The reduced coenzymes enter
the electron transport chain,
which consists of a system
(chain) of protein complexes
found in the inner membrane
of the mitochondria. These
proteins accept the electrons
from NADH and pass them
along the chain to the
terminal electron acceptor,
molecular oxygen, which is
reduced to water.
ethanol
This process does not yield any ATP; however, it does serve to convert
NADH back to NAD+, which can then be fed back into glycolysis. Once
NAD+ has been regenerated, glycolysis can continue. As glycolysis results
in a net production of only two molecules of ATP, anaerobic respiration
yields only a small amount of energy compared with aerobic respiration,
which yields 36 molecules of ATP per molecule of glucose.
Under aerobic conditions, pyruvate enters the mitochondria (rodshaped organelles, in which most of the energy is produced in the cell).
Through a complex series of reactions and steps, pyruvate is ultimately
oxidised to carbon dioxide, while oxygen is reduced to water.
The electron transport chain

It is the electron transport chain that generates the largest amount of
ATP molecules. This is a series of proteins in the inner mitochondrial
membrane that act as electron carriers, passing electrons from reduced
coenzymes along the chain to molecular oxygen. It consists of a series of
redox reactions, involving the flow of electrons from a reducing agent to
an oxidising agent. The electrons flow along the chain in the direction
of increasing electrode potential (reduction potential), i.e., passed
from a stronger reducing agent to a stronger oxidising agent, with the
ultimate reduction of oxygen to water (Figure B43).
strongest reducing agent
strongest oxidising agent
O2
NADH
e
NAD+
electron transport chain
H2O
Figure B43 Representation of the electron transport chain.
The NADH coenzymes are strong reducing agents and give up their
two electrons to the first protein complex in the chain. They are oxidised
back to NAD+ for reuse, and hydrogen ions (H+) are generated in this
process. The electrons are passed on to an electron carrier (which accepts
the electrons, i.e. gets reduced) and passes them on to the next protein
complex along the chain until the terminal oxidising agent (O2) is
reached. The equation for the reduction of oxygen is as follows:
O2 + 4e + 4H+ 2H2O
As the electrons are passed from one carrier to the next, hydrogen ions
are pumped into the space between the inner and outer mitochondrial
membranes. When the hydrogen ions flow back through the membrane (via
a protein channel), energy is released, which drives the synthesis of ATP.
Electron carriers
Many of the proteins in the electron transport chain are cytochromes.
Cytochromes act as electron carriers; they contain a prosthetic (nonprotein) group called a porphyrin, which is a large ring structure
46
consisting of four rings linked together. Most porphyrins have Fe at their HL

centre, in which case it is known as a haem group (heme in the USA).
Some cytochromes, such as cytochrome oxidase (the enzyme that reduces
oxygen to water in the electron transport chain), also contain Cu. When
cytochrome oxidase accepts electrons from the preceding electron carrier
in the chain (which acts as a reducing agent and gets oxidised), the Fe and
Cu change their oxidation states:
Cu2+ is reduced to Cu+ (Cu2+ + e Cu+)
Fe3+ is reduced to Fe2+ (Fe3+ + e Fe2+)
Cytochrome oxidase now acts as a reducing agent and gets oxidised: it
passes the electrons on to the terminal electron acceptor, oxygen, which is
reduced to water:
Cu+ is oxidised to Cu2+ (Cu+ Cu2+ + e)
Fe2+ is oxidised to Fe3+ (Fe2+ Fe3+ + e)
Electrons transferred to oxygen:
O2 + 4e + 4H+ 2H2O
Oxygen carriers
As well as transporting electrons, haem-containing proteins also play an
essential role in transporting oxygen: haemoglobin transports oxygen
from the lungs through the bloodstream and releases it to the cells of the
tissues, to carry out respiration.
Haemoglobin consists of four polypeptide sub-units, each of which
contains a haem prosthetic group with the iron at the centre of the
haem in the Fe2+ oxidation state (Figure B44). Each haem can carry one
CH2
CH
H3C
H3C
HC
CH
N
N
H2C
CH2
2+
Fe
CH3
N
CH
N
HC
CH
CH2
COO
H2C
CH3
CH2
COO
Figure B44 The structure of haem in haemoglobin.
47
HL molecule of oxygen; therefore, each haemoglobin molecule can transport
four molecules of oxygen.

Oxygen binds to haemoglobin reversibly.The haem Fe can bond to six
ligands. In the unbound state, the Fe2+ is bonded to five ligands: four ligands
are the pyrrole nitrogens of the porphyrin and one ligand is an amino acid
that attaches it to the protein.When molecular oxygen binds, this becomes
the sixth ligand, and haemoglobin is said to be oxygenated (it is this
oxygenated form that gives blood its red colour, owing to the red colour
of the haem prosthetic group). In haemoglobin, the oxygen only binds
reversibly, allowing its release to tissue cells, to be used in cellular respiration.
Test yourself
20 Use oxidation numbers to deduce whether the conversion
shown below involves oxidation or reduction or both:
H
O
+ H+
H + CO2
pyruvate
ethanal
Exam-style questions
1 The energy value of foods can be obtained using a food (bomb) calorimeter. A 2.6 g sample of salmon was
burnt in a food calorimeter containing 250 g water. It raised the temperature of the water from 20.4 C
to 26.0 C. The specific heat capacity of water is 4.18 J g1 K1.
a How much energy (in kJ) is contained in 250 g of salmon?
[2]
b Give one reason why the result obtained was not completely accurate.
[1]
2 Immunoglobulin G is an antibody that plays an important role in the immune system. It is a protein made
up of four polypeptide sub-units.
a The polypeptides in immunoglobulin G are made up from 2-amino acids.
i Give the general structural formula for 2-amino acids.
ii Describe two other characteristic properties of 2-amino acids.
[1]
[2]
b Explain what is meant by the primary structure of a polypeptide chain and name the type of bond
that links the amino acids together in the primary structure.
[2]
48
i Draw the structural formula of one of the dipeptides formed when glycine reacts with cysteine
(structures are given in the IBO Chemistry Data booklet) and name the type of reaction occurring.
ii Explain why it is possible to form more than one dipeptide when glycine reacts with cysteine.
[2]
[2]
d How many possible tripeptides could be produced by reacting glycine, cysteine and serine? Draw one
of these tripeptides.
[2]
e The amino acids in the immunoglobulin can be analysed using paper chromatography.
i Why is the immunoglobulin first treated with dilute hydrochloric acid before paper chromatography
is carried out?
ii Describe how paper chromatography is used to analyse amino acids.
[1]
[4]
3 Carbohydrates are the most abundant class of biological molecules and include simple sugars as well as
complex polysaccharides.
a Glucose is the monosaccharide that makes up starch; draw its straight-chain structure.
[1]
b Glucose can form two cyclic isomers. Explain why this occurs and name both isomers.
[3]
c Name the two different types of polysaccharides found in starch and name the types of linkages that join
the glucose units together in each form.
[3]
d State the type of reaction that occurs when two glucose units join together to form a disaccharide and
name the other product of the reaction.
[2]
e Cellulose is also a polysaccharide made up of glucose units. Explain why humans, and most other animals,
cannot digest cellulose.
[2]
4 Lipids play important roles in the body.

a
i Define the term iodine number.

ii If 11.43 g of I2 reacts with 0.015 mol of a fatty acid, explain what can be deduced about the structure
of this fatty acid (Mr for I2 = 253.8 g mol1).
[1]
[3]
b Write an equation to represent the reaction between fatty acids and glycerol to produce a triglyceride
(the hydrocarbon chains can be represented by R).
[3]
c Explain how the composition of fatty acids in fats and oils affects their melting point.
[3]
d Explain what an omega-3 fatty acid is and why an adequate dietary intake is important.
[3]
e State one role of cholesterol in the body and describe how it is transported through the body.
[3]
5 a The structures of ascorbic acid (vitamin C) and retinol (vitamin A) are shown below. Explain whether
they are fat- or water-soluble vitamins.
[2]
CH2OH
CH
HO
H
HO
OH
ascorbic acid (vitamin C)
H3C
CH3
CH3
H
C
CH3
C
H
CH3
C
H
H
C
C
H
C
H
CH2OH
retinol (vitamin A)
b Describe the effect of a deficiency of vitamin A and suggest two possible solutions to overcome
the problem.
[3]
49
6 Hormones are chemical messengers.

a Name the characteristic structural feature found in the sex hormones, testosterone and oestradiol
(structures are given in the IBO Chemistry Data booklet).
[1]
b Identify two differences in the structures of testosterone and oestradiol, with respect to functional groups.
[2]
c Describe how the combined oral contraceptive pill prevents pregnancy.
[2]
d State where the hormone insulin is produced in the body and describe its main effect on the body.
[2]
HL 7 Enzymes catalyse almost every biochemical reaction in the body.
a Describe, in general terms, how enzymes catalyse biochemical reactions.
[3]
b Many medicinal drugs act by inhibiting enzymes in the body, either non-competitively or, more
commonly, competitively.
i Describe how competitive inhibitors work and how these differ from non-competitive inhibitors.
ii What effect does increasing the substrate concentration have on each type of inhibitor?
iii How does each type of inhibitor affect the Vmax and Km?
[2]
[2]
[2]
c Describe two differences between enzymes and inorganic catalysts.
[2]
8 a The structures of four nucleotide bases are given below. Draw the two sets of base pairs that are found
in DNA, including the hydrogen bonds that form between them.
H
N
HN
H
HN
N
N
guanine (G)
[3]
N
N
adenine (A)
H
O
H
CH3
N
N
NH
O
thymine (T)
NH
O
cytosine (C)
b State two structural differences between DNA and RNA.

9 Cytochrome oxidase is an enzyme involved in aerobic respiration. Describe the role played by cytochrome
oxidase in aerobic respiration, including the role of the copper ions. Use suitable equations to illustrate
your answer.
50
[2]
[5]

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B Human biochemistry

Calculate the energy value

Draw the general structure of

The general chemical formula of a 2-amino acid can be written as:

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

Acidbase behaviour of 2-amino acids

Figure B2 Diagram showing the numbering

The central carbon atom is also

The word zwitterion comes

Figure B3 Formation of a zwitterion.

The pH at which this zwitterion exists is known as the isoelectric

Figure B4 Changes in charges on the amino acid as pH increases.

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

Amino acids can act as buffers

A buffer solution is one that resists

The full explanation is a bit

The systematic name of glycine is

Types of amino acid

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

Condensation reaction: two

The amide functional group is:

Figure B6 Formation of two possible dipeptides.

The dipeptides are different depending on which way around the

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

Figure B7 Condensation reaction between a dipeptide and an amino acid to form a

Five other tripeptides could be

Figure B8 Structure of the tripeptide GlyCysSer.

Secondary structure of proteins

Figure B9 (a) -helix; (b) -pleated sheet.

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

The -pleated sheet

sheets consist of two or more stretches of amino acids in which

Tertiary structure of proteins

The precise sequence of amino

van der Waals

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

Quaternary structure of proteins

provide support and strength

collagen (most abundant protein in body;

enzymes catalyse biochemical reactions within the body

salivary amylase (involved in starch digestion),

have a regulatory effect on specic cells/organs in the body

insulin (regulates blood glucose levels), growth

immunological play a key role in the ght against infection

antibodies (recognise and bind to foreign

carry materials around the body

haemoglobin (transports oxygen), serum

proteins are broken down to amino acids in the body, which

Table B1 Functions of proteins in the body.

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

This is also discussed in Option A

Figure B11 Separation of amino acids using paper chromatography.

distance travelled by spot

The Rf value is always 1 or less.

To give an example, in Figure B11, the distance to the top spot is

7 The isoelectric point for alanine is at pH 6.15.

6 If an amino acid has an Rf value of 0.92, is it likely

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

The ring form of monosaccharides

Describe the common structural

Monosaccharides have the

CHEMISTRY FOR THE IB DIPLOMA CAMBRIDGE UNIVERSITY PRESS 2011

(carbon 1 in glucose) joins to carbon 5 via a bridging O atom. However,