2

Molecular biology
Chapter summary a reminder of the issues to be revised
Notes

Metabolism, all the chemical reactions of life, consists

of anabolic reactions, the construction of complex
molecules from smaller ones, for example protein
synthesis, and catabolic reactions, the breakdown of
complex molecules, for example oxidation of sugar
in respiration. All reactions of metabolism are made
possible by enzymes. Enzymes are biological catalysts,
most made of protein. Enzymes are highly specific to the
type(s) of substrate molecule and type of reaction that
they catalyse.

Organic compounds contain the elements carbon and

hydrogen, usually with oxygen and other elements.
Carbon atoms form strong, covalent bonds (sharing
electrons between atoms) with other carbon atoms
and with atoms of other elements, forming a huge
range of compounds. Many of the organic compounds
of life fall into one of the four groups of compounds:
carbohydrates, lipids, proteins or nucleic acids.

Water is electrically neutral but, because of its shape, it

carries an unequal distribution of charge it is a polar
molecule (oxygen with a negative charge, hydrogen with
a positive charge). Consequently, water forms hydrogen
bonds with other water molecules. These hydrogen
bonds are responsible for the properties of water that
are important to life water is the medium of life.

Carbohydrates contain carbon, hydrogen and oxygen

only, and have the general formula of Cx(H2O)y.
They consist of the sugars (monosaccharides and
disaccharides) and macromolecules built from sugars
(polysaccharides).

Monosaccharides include the 6-carbon sugars (hexoses),

e.g. glucose, and are important energy sources for
cells. The hexoses have the same molecular formula
(C6H12O6) but different structural formulae. Two
hexose monosaccharides combine together with the
removal of water (a condensation reaction) to form a
disaccharide sugar, held together by a glycosidic bond.
The disaccharide sucrose combines glucose and fructose.
Monosaccharides (and some disaccharides) are reducing
sugars; when heated with alkaline copper II sulfate
(Benedicts solution blue) they produce reduced
copper I oxide, which is a brick red precipitate. The
sugar is oxidized to a sugar acid. Sucrose is not a reducing
sugar.

Most polysaccharides are built from glucose units

condensed together. They are examples of polymers
consisting of a huge number of monomers (such
as glucose) condensed together. They may be food
stores (starch, glycogen) or structural components of
organisms (cellulose, chitin).
Biology for the IB Diploma, Second edition C. J. Clegg 2014 Published by Hodder Education

Chapter summary
Notes

Lipids the fats (and oils) contain the elements

carbon, hydrogen and oxygen where the proportion of
oxygen is low. They are hydrophobic and insoluble in
water, but otherwise form a diverse group of compounds.
Fats and oils leave a cloudy white suspension in the
emulsion test. Fats are formed by condensation reaction
between the hydroxyl groups of glycerol and three fatty
acids, forming a triglyceride, with ester bonds. The
fatty acids may be saturated or unsaturated (containing
double bonds between carbon atoms in the hydrocarbon
tails). Fats and oils are effectively energy stores.

In phospholipids, one of the hydroxyl groups of

glycerol reacts with phosphoric acid. The product has a
hydrocarbon tail (hydrophobic) and an ionized phosphate
group (hydophilic), so they form bilayers on water, and
form the membranes of cells (along with proteins).

Proteins contain nitrogen and (often) sulfur, in addition

to carbon, hydrogen and oxygen. The building blocks
of proteins are amino acids, and many hundreds or
thousands of amino acid residues form a typical protein.
Amino acids have a basic amino group (NH2) and an
acidic carboxyl group (COOH) attached to a carbon
atom to which the rest of the molecule (R) is also
attached. Of the many amino acids that occur, only 20
are used to make the proteins of living things, Amino
acids combine by peptide bonds between the carboxyl
group of one molecule and the amino group of the other
to form a polypeptide chain. Proteins, too, are polymers.

10

The properties of polypeptides and proteins are

determined by the amino acids they are built from and
the sequence in which the amino acids occur. The
sequence of amino acids is the primary structure of the
protein, and is indirectly controlled by the nucleus. The
shape the protein molecule takes up also determines its
properties. Part of a polypeptide chain may form into a
helix and part into sheets (the secondary structure of a
protein). The whole chain is held in position by bonds
between folded parts, forming the tertiary structure of
a protein. Separate polypeptide chains may combine,
sometimes with other substances, to form the quaternary
structure.

11

Some proteins have a structural role and are fibrous

proteins, for example collagen of skin, bone and tendon.
Many proteins are enzymes or antibodies (and some are
hormones), and these are globular proteins. Enzymes
work by forming a temporary complex with a substrate
molecule at a special part of the enzyme surface, called
the active site (lock and key hypothesis). Enzymes work
by lowering the activation energy needed for a reaction
to occur. A slight change in shape of the substrate
molecule when docked at the active site helps raise the
molecule to a transition state (induced fit hypothesis),
from which the products may form. The enzyme is
released for reuse.

Biology for the IB Diploma, Second edition C. J. Clegg 2014 Published by Hodder Education

Chapter summary
Notes

12

The rate of an enzyme-catalysed reaction is found

by measuring the disappearance of the substrate or
the accumulation of the product in unit time. The
initial rate of reaction is taken, since the reaction
rate falls with time. The factors that affect the rate
of an enzyme-catalysed reaction include pH and
temperature, through their effects on protein structure.
When molecules of inhibitors are in contact with
enzyme molecules, the rate of reaction may be lowered in
characteristic ways.

13

Nucleic acids consists of 5-carbon sugars and phosphate,

which alternate in a long backbone. To each sugar is
also attached a nitrogenous base. Sugar, phosphate and
an organic base form a nucleotide, so a length of nucleic
acid is a polynucleotide. The bases are often referred to
by their initials (C and G, A and T or U).

14

There are two forms of nucleic acid, DNA and RNA.

DNA and RNA differ in the 5-carbon sugar they
contain, in the bases they contain, and in their roles
in cells. DNA exists as a double strand in the form of
a helix. RNA is single-stranded. DNA occurs in the
nucleus, and RNA in the nucleus and cytoplasm.

15

DNA stores the genetic code (information), which can

be copied to the cell to direct protein synthesis, and
also copied to pass on to new cells. RNA, in the form of
messenger RNA, carries the base sequence of the gene to
the cytoplasm where it is used as a template for protein
synthesis in an organelle called a ribosome. Other
forms of RNA are involved in bringing the amino acids
together in the correct sequence at the ribosome.

16

Respiration is a cellular process in which energy is

transferred from nutrients, such as glucose, to the
cellular machinery. Energy is required to do useful work,
such as the transport of metabolites across membranes,
the driving of anabolic reactions and to cause
movements in organisms. Aerobic respiration involves
the complete oxidation of glucose to carbon dioxide and
water, with the releases of a large amount of energy. In
addition to hexose sugar, fats and proteins may be used
as respiratory substrates. Anaerobic respiration involves
the partial oxidation of glucose with the release of only
a small amount of energy. ATP is the universal energy
currency molecule by which energy is transferred to
do useful work. ATP is a soluble molecule, formed in
the mitochondria but able to move into the cytosol by
facilitated diffusion. It diffuses freely about cells.

17

The rate of aerobic respiration can be measured

manometrically, in a respirometer. The respiratory
quotient (RQ) is the ratio of the volume of carbon
dioxide produced to the volume of oxygen used, in a
given time. The RQ is an indicator of the respiratory
substrate.

Biology for the IB Diploma, Second edition C. J. Clegg 2014 Published by Hodder Education

Chapter summary
Notes

18

In anaerobic respiration, the products are either lactate

(in lactic acid fermentation, typically found in vertebrate
muscle) or ethanol and carbon dioxide (in alcoholic
fermentation, found in yeast and in plants under
anaerobic conditions). Anaerobic respiration is wasteful
of respiratory substrate. It yields only a tiny quantity
of ATP, when compared with the yield of ATPs from
aerobic respiration of the same quantity of respiratory
substrate. The waste products, ethanol or lactic acid,
contain much unused chemical energy. They are both
energy-rich molecules.

19

Photosynthesis is an energy transfer process in

which green plants manufacture carbohydrates from
carbon dioxide and water, using energy from sunlight.
Oxygen is the waste product. Chloroplasts, the
organelles in which photosynthesis occurs, are chiefly
found in mesophyll cells of the leaves, particularly the
palisade mesophyll cells. Plants use the products of
photosynthesis to manufacture the other carbohydrates,
lipids, proteins and all other metabolites, enzymes and
pigments required. For this, they require energy from
respiration and selected mineral ions, absorbed from
the soil. Consequently, plant nutrition is described as
autotrophic (self-feeding).

20

Chlorophyll consists of a mixture of pigments, two

of which are chlorophylls. They can be separated by
chromatography. Measurements of the absorption
spectrum of chlorophyll and the action spectrum
of photosynthesis show that it is the blue and red
components of white light that are selectively absorbed
and are most effective in bringing about photosynthesis.

21

In green plants the volume of oxygen-enriched gas

given off in the light is a measure of the rate of
photosynthesis. The volume of gas produced by aquatic
plants under different conditions can be measured
in a microburette (photosynthometer) apparatus. As
photosynthesis consists of a number of interconnected
reactions, the slowest will determine the overall rate.
It is then described as a limiting factor. A limited supply
of either carbon dioxide or light will limit the overall
rate of photosynthesis, since both are essential for
photosynthesis.

Biology for the IB Diploma, Second edition C. J. Clegg 2014 Published by Hodder Education

Data handling questions

The answers for
factual recall
questions are
available online.
Other questions
are designed to be
tackled alone or
in groups, where
the outcomes can
be discussed with
peers or tutors, for
example, or done as a
homework activity.

Data handling questions

The effect of pH on the activity of an enzyme
Change in pH can have a dramatic effect on the rate of an enzyme-catalysed reaction.
Thetable below gives the results a student obtained, working with two enzymes that catalyse
the hydrolysis of proteins. These protease enzymes were (1) pepsin and (2) trypsin. The initial
rates of reaction were measured at a range of pH values.
pH
initial
rate

1
pepsin
trypsin

2
4.0

3.0

3
4.5

4
3.3
0.5

5
0.8
2.0

10

11

4.0

5.0

5.2

4.0

3.0

0.5

1 Present these results by means of a graph following the rules and guidance given in
Appendix 2 (pages 45).
2 How is an initial rate of reaction measured at each pH value?
3 Of the data recorded above, which is
a the dependent variable
b the independent variable?
4 How would you describe
a the general effect of varying pH on these enzyme-catalysed reactions
b the specific effects of pH on pepsin and trypsin?
5 Why do changes in pH have the effects they do on the activity of enzymes?

Changing light intensity and the rate of photosynthesis

The results of an experiment to determine the effect on varying the light intensity on the rate
of photosynthesis (oxygen production) at different fixed carbon dioxide concentrations are
recorded in the table below.
The effect on the
rate of photosynthesis
(oxygen production)
of varying light
intensities at low and
high carbon dioxide
concentrations

Light
intensity
(arbitary
units)
low CO2
conc.
(arbitary
units)
high CO2
conc.
(arbitary
units)

10

11

12

1.0

0.8

2.5

4.2

6.0

6.2

6.1

6.4

6.3

6.3

6.4

6.2

6.4

1.0

1.0

2.8

4.1

6.1

7.5

9.5

11.2

11.8

11.6

11.5

11.9

11.9

1 Sketch and annotate a diagram of the apparatus you might use to conduct a similar
experiment.
2 Plot an appropriate graph of these results.
3 Explain the negative result obtained at the lowest light intensity.
4 Deduce why the curves for low and high carbon dioxide concentrations were the same
between 1 and 4 units of light intensity.
5 Explain what is limiting the rate of photosynthesis at higher carbon dioxide concentration
a between 5 and 7 units of light intensity
b between 8 and 12 units of light intensity.

Biology for the IB Diploma, Second edition C. J. Clegg 2014 Published by Hodder Education

Do and understand activities

Do and understand activities

Complete the text
Review the following passage then make a list of the missing words.
Many different chemical elements make up the Earth. Only 16 of these elements are
1
and
essential for life, and just four of them, carbon, hydrogen,
2
make up 95% of all living matter. Compounds built from carbon
3
are called
. Carbon is not a common element of the
Earths crust, but in living things carbon is the second most abundant element by mass. Why
is carbon so important to life?
The answer is that carbon has a unique collection of properties, so remarkable that they make
life possible.
n

4
Carbon is a relatively small
, able to form four strong,
5
stable bonds called
bonds. Carbon atoms form these
6
bonds by
pairs of electrons with neighbouring atoms.
They are the strongest bonds that occur in biological molecules; a great deal of
8
7
has to be
to break them.

9
Carbon atoms are able to react with
to
form extended chains. These carbon skeletons may be straight chains, branched
10
chains or
. So, a vast number of extremely stable carbon
11
exist.

12
The four bonds of carbon atoms point to the corners of a regular
(a pyramid with a triangular base). This is because the four pairs of electrons
13
each other, and so position themselves away from each other,
as far as possible.

Carbon atoms form

15
hydrogen,
with distinctive properties.

Carbon compounds, although numbering 23 million in total, fit into a relatively small
numbers of families. Members of a family are identified by a part of their molecule
16
that is known as the
which gives them
their characteristic chemical properties. The remainder of the molecule has little or no
17
effect on the chemical properties and is referred to as the
.
18
.

Two carbon atoms can sometimes form two bonds between them, referred to as a
19
bond. Carbon compounds that contain these bonds are
20
known as
compounds.

14

bonds with other atoms, such as oxygen,

and sulfur, forming different groups of molecules

Water as a polar molecule

Water makes up about 80% of the cell contents; it is the environment for the chemical
reactions of life. It is a substance we might take for granted, yet its structure and properties
are unusual. Two hydrogen atoms are combined with an oxygen atom by sharing of electrons
(covalent bonding), but the molecule is triangular rather than linear. Within the molecule,
the oxygen nucleus draws electrons (negatively charged) away from the hydrogen nuclei
(positively charged). So, overall, the water molecule is electrically neutral, but there is a net
negative charge on the oxygen atom and a net positive charge on the hydrogen atoms. A
molecule carrying such an unequal distribution of electrical charge is called a polar molecule.
When a burette is filled with water and the tap opened, a fine jet of water flows and the water
can be collected in a jar or beaker. If a plastic rod is rubbed with a dry cloth, the rod becomes
charged with static electricity. For example, a polythene rod becomes negatively charged; a
Perspex rod becomes positively charged.

Biology for the IB Diploma, Second edition C. J. Clegg 2014 Published by Hodder Education

Do and understand activities

When such charged rods are held close to the water jet, it becomes deflected. The effects
of rods charged to varying extents can be investigated. As a control you can set up another
burette with a non-polar liquid of approximately the same viscosity (such as paraffin heating
oil) and attempt to repeat the same demonstration.
1 Make an annotated sketch of the effects observed in the experiment described above.
2 List the important properties of water that are due to its polar nature.

Table of the differences between DNA and RNA

DNA and RNA are two types of nucleic acid with many features of structure in common, but
with highly significant differences. By means of a table like the one shown below, compare
DNA and RNA, by making reference to the key features of their structure, location in cells
and composition. Information on the functions and roles of these information molecules is
not required in this table.
DNA

RNA

Biology for the IB Diploma, Second edition C. J. Clegg 2014 Published by Hodder Education

Further study

Further study
Web resource
RasMol, the molecular visualization software, at:
www.umass.edu/microbio/rasmol/

Further reading
Articles in recent editions of Biological Sciences Review:

What is tertiary structure?, 21.1, pp.1013 (September 2008)

Water, life and hydrogen bonding, 21.2, pp.1820 (November 2008)
Enzymes: natures catalytic machines, 22.2, pp.2225 (November 2009)
Metals in proteins, 23.2, pp.1619 (November 2010)

Biology for the IB Diploma, Second edition C. J. Clegg 2014 Published by Hodder Education