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Chapter 1
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Cell structure rs
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LEARNING INTENTIONS
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In this chapter you will learn how to:

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• explain that cells are the basic units of life

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• use the units of measurement relevant to microscopy

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• recognise the common structures found in cells as seen with a light microscope and outline their
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structures and functions

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• compare the key structural features of animal and plant cells

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• use a light microscope and make temporary preparations to observe cells

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• recognise, draw and measure cell structures from temporary preparations and micrographs
• calculate magnifications of images and actual sizes of specimens using drawings or micrographs
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• explain the use of the electron microscope to study cells with reference to the increased resolution of
electron microscopes
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• recognise the common structures found in cells as seen with an electron microscope and outline their
structures and functions
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• outline briefly the role of ATP in cells

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• describe the structure of bacteria and compare the structure of prokaryotic cells with eukaryotic cells
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• describe the structure of viruses.

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CAMBRIDGE INTERNATIONAL AS & A LEVEL BIOLOGY: COURSEBOOK

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BEFORE YOU START

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• Make a list of structures that could be found in a cell.

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• Try to write down the functions of the structures you have listed.
• Which structures are found in plant cells and which are found in animal cells?
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• Are there any cells that are not animal or plant cells?
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THINKING OUTSIDE THE BOX

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Progress in science often depends on people

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thinking ‘outside the box’ – original thinkers who

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are often ignored or even ridiculed when they

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first put forward their radical new ideas. One such

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individual, who battled constantly throughout
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her career to get her ideas accepted, was the

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American biologist Lynn Margulis (1938–2011;

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Figure 1.1). Her greatest achievement was to use

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evidence from microbiology to help firmly establish

am

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an idea that had been around since the mid-19th
century – that new organisms can be created from
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combinations of existing organisms. Importantly,

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the existing organisms are not necessarily closely

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related. The organisms form a symbiotic partnership

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(they live together in a partnership in which both

partners benefit). Margulis imagined that one
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organism engulfed (‘ate’) another. Normally the

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engulfed organism would be digested and killed, Figure 1.1: Lynn Margulis: ‘My work more than didn’t fit
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but sometimes the organism engulfed may survive in. It crossed the boundaries that people had spent their
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and even be of benefit to the organism in which lives building up. It hits some 30 sub-fields of biology,
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it finds itself. This type of symbiosis is known as even geology.’

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endosymbiosis (‘endo’ means inside). A completely

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new type of organism is created, representing a traditional view, first put forward by Charles Darwin,
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dramatic evolutionary change. that evolution occurs mainly as a result of

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competition between species.

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The best-known example of Margulis’ ideas is her

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suggestion that mitochondria and chloroplasts Questions for discussion

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were originally free-living bacteria (prokaryotes). • Can you think of any ideas people have had
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She suggested that these bacteria invaded the which were controversial at the time but
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ancestors of modern eukaryotic cells, which are

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are now accepted? Try to think of scientific

much larger and more complex cells than bacteria,
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examples. You may also like to consider why

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and entered into a symbiotic relationship with the ideas were controversial.
the cells. This idea has been confirmed as true by
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later work. Margulis saw such symbiotic unions • Can you think of any scientific ideas people
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as a major driving cause of evolutionary change. have now which are controversial and not
accepted by everybody?
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Throughout her life, she continued to challenge the

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1 Cell structure

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animals. It was soon also realised that all cells come from
1.1 Cells are the basic

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pre-existing cells by the process of cell division. This

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raises the obvious question of where the original cell

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units of lifeam came from. There are many hypotheses, but we still have

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no definite answers to this question.
Towards the middle of the 19th century, scientists made a
fundamental breakthrough in our understanding of how life
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‘works’. They realised that the basic unit of life is the cell. Why cells?

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The origins of this idea go back to the early days of

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A cell can be thought of as a bag in which the chemistry
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microscopy when an English scientist, Robert Hooke, of life occurs. The activity going on inside the cell is
decided to examine thin slices of plant material. He

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therefore separated from the environment outside the cell.

chose cork as one of his examples. Looking down the The bag, or cell, is surrounded by a thin membrane. The
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microscope, he made a drawing to show the regular membrane is an essential feature of all cells because it
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appearance of the structure, as you can see in Figure 1.2.

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controls exchange between the cell and its environment.
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In 1665 he published a book containing

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It can act as a barrier, but it can also control movement

this drawing.
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of materials across the membrane in both directions. The

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membrane is therefore described as partially permeable.
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If it were freely permeable, life could not exist, because

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the chemicals of the cell would simply mix with the

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surrounding chemicals by diffusion and the inside of the

cell would be the same as the outside.
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Two types of cell

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During the 20th century, scientists studying the cells

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of bacteria and of more complex organisms such as

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plants and animals began to realise that there were

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two fundamentally different kinds of cells. Some cells

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were very simple, but some were much larger and more
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complex. The complex cells contained a nucleus (plural:

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nuclei) surrounded by two membranes. The genetic

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material, DNA, was in the nucleus. In the simple cells

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the DNA was not surrounded by membranes, but

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apparently free in the cytoplasm.

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Figure 1.2: Drawing of cork cells published by Robert

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KEY WORDS
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Hooke in 1665.
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cell: the basic unit of all living organisms; it is

surrounded by a cell surface membrane and
If you examine the drawing you will see the regular
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contains genetic material (DNA) and cytoplasm

structures that Hooke called ‘cells’. Each cell appeared
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containing organelles
to be an empty box surrounded by a wall. Hooke had
y

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discovered and described, without realising it, the organelle: a functionally and structurally distinct
fundamental unit of all living things. part of a cell, e.g. a ribosome or mitochondrion
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Although we now know that the cells of cork are dead, nucleus (plural: nuclei): a relatively large
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Hooke and other scientists made further observations of organelle found in eukaryotic cells, but absent
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cells in living materials. However, it was not until almost from prokaryotic cells; the nucleus contains the
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200 years later that a general cell theory emerged from

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cell’s DNA and therefore controls the activities

the work of two German scientists. In 1838 Schleiden,
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of the cell; it is surrounded by two membranes

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a botanist, suggested that all plants are made of cells. A which together form the nuclear envelope
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year later Schwann, a zoologist, suggested the same for

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Organisms made of cells with membrane-bound are unfamiliar to most people. Before studying light and

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nuclei are now known as eukaryotes, while the simpler electron microscopy further, you need to become familiar

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cells lacking membrane-bound nuclei are known as with these units.

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prokaryotes (‘eu’ means true, ‘karyon’ means nucleus,
am According to international agreement, the International

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‘pro’ means before). Eukaryotes are thought to have
System of Units (SI units) should be used. In this system,
evolved from prokaryotes more than two billion years
the basic unit of length is the metre (symbol, m). More
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ago. Prokaryotes include bacteria. Eukaryotes include

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units are created by going a thousand times larger or

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animals, plants, fungi and some other organisms.
smaller. Standard prefixes are used for the units. For
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example, the prefix ‘kilo’ means 1000 times. Thus,
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KEY WORDS 1 kilometre = 1000 metres. The units of length relevant

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to cell studies are shown in Table 1.1.

eukaryote: an organism whose cells contain a

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nucleus and other membrane-bound organelles The smallest structure visible with the human eye is
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about 50–100 μm in diameter (roughly the diameter of

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prokaryote: an organism whose cells do not
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the sharp end of a pin). The cells in your body vary in

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contain a nucleus or any other membrane-bound size from about 5 μm to 40 μm. It is difficult to imagine
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organelles

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how small these cells are, especially when they are clearly
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visible using a microscope. An average bacterial cell is

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about 1 µm across. One of the smallest structures you

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will study in this book is the ribosome, which is only

1.2 Cell biology and
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about 25 nm in diameter! You could line up about

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microscopy this sentence.
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The study of cells has given rise to an important branch

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of biology known as cell biology. Cell biologists study

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1.3 Plant and animal

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cells using many different methods, including the use of

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various types of microscope.

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There are two fundamentally different types of cells as seen with a light
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microscope: the light microscope and the electron

microscope
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microscope. Both use a form of radiation in order to

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see the specimen being examined. The light microscope

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uses light as a source of radiation, while the electron Microscopes that use light as a source of radiation are
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microscope uses electrons, for reasons which are called light microscopes. Figure 1.3 shows how the light
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discussed later. microscope works.

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Note: the structure of a light microscope is

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Units of measurement extension content, and is not part of the syllabus.

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In order to measure objects in the microscopic world,

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we need to use very small units of measurement, which

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Fraction of a metre Unit Symbol

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–3
one thousandth = 0.001 = 1/1000 = 10 millimetre mm
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–6
one millionth = 0.000 001 = 1/1000 000 = 10 micrometre μm
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one thousand millionth = 0.000 000 001 = nanometre nm

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1/1000 000 000 = 10–9

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Table 1.1: Units of measurement relevant to cell studies: 1 micrometre is a thousandth of a millimetre; 1 nanometre is a
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thousandth of a micrometre.
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1 Cell structure

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Eyepiece lens magnifies and showing the structure of a generalised plant cell, both

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eyepiece
focuses the image from the as seen with a light microscope. (A generalised cell

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objective onto the eye. shows all the structures that may commonly be found

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in a cell.) Figures 1.6 and 1.7 are photomicrographs.
light beam am

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A photomicrograph is a photograph of a specimen as
seen with a light microscope. Figure 1.6 shows some
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human cells. Figure 1.7 shows a plant cell taken from a

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leaf. Both figures show cells magnified 400 times, which
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objective Objective lens collects light is equivalent to using the high-power objective lens on

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coverslip passing through the specimen a light microscope. See also Figures 1.8a and 1.8b for
and produces a magnified image. labelled drawings of these figures.

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glass slide
Many of the cell contents are colourless and transparent

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Condenser lens focuses the so they need to be stained with coloured dyes to be seen.
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condenser
light onto the specimen held The human cells in Figure 1.6 have been stained. The

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between the coverslip and slide.

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iris diaphragm chromatin in the nuclei is particularly heavily stained.
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The plant cells in Figure 1.5 have not been stained

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light source Condenser iris diaphragm is
because the chloroplasts contain the green pigment
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closed slightly to produce a

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pathway of light narrow beam of light.
chlorophyll and are easily visible without staining.

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Figure 1.3: How the light microscope works. The coverslip is

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a thin sheet of glass used to cover the specimen. It protects

Question
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specimens from drying out and also prevents the objective
lens from touching the specimen. 1 Using Figures 1.4 and 1.5, name the structures that:
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a animal and plant cells have in common

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small structures that b are found only in plant cells

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Golgi apparatus
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are difficult to identify

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c are found only in animal cells.

cytoplasm
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Features that animal and plant

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mitochondria
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cells have in common

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Cell surface membrane

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cell surface All cells, including those of both eukaryotes and

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membrane prokaryotes, are surrounded by a very thin cell surface

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membrane. This is also sometimes referred to as the

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plasma membrane. As mentioned before, it is partially

permeable and controls the exchange of materials
am

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between the cell and its environment.

nuclear envelope
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Nucleus
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chromatin –
centriole – always deeply staining
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nucleus All eukaryotic cells contain a nucleus. The nucleus

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found near nucleus and thread-like

is a relatively large structure. It stains intensely and
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nucleolus –
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deeply staining
KEY WORD
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Figure 1.4: Structure of a generalised animal cell (diameter

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about 20 μm) as seen with a very high quality light cell surface membrane: a very thin membrane
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microscope. (about 7 nm diameter) surrounding all cells; it is

partially permeable and controls the exchange of
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Figure 1.4 is a drawing showing the structure of a materials between the cell and its environment
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generalised animal cell and Figure 1.5 is a drawing

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middle lamella – thin layer

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tonoplast – membrane
holding cells together

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surrounding vacuole

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am cell surface membrane plasmodesma –

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(pressed against cell wall) connects cytoplasm
of neighbouring cells
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vacuole – large cell wall of

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with central position neighbouring
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cell
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cytoplasm

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cell wall

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mitochondria
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chloroplast

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nucleolus –
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grana just visible

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deeply staining

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nuclear envelope
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nucleus

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chromatin – small structures that

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deeply staining are difficult to identify

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and thread-like Golgi apparatus

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Figure 1.5: Structure of a generalised plant cell (diameter about 40 μm) as seen with a very high quality light microscope.
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Figure 1.6: Cells from the lining of the human cheek (×400). Figure 1.7: Cells in a moss leaf (×400). Many green chloroplasts
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Each cell shows a centrally placed nucleus, which is typical are visible inside each cell. The grana are just visible as black
R

of animal cells. The cells are part of a tissue known as grains inside the chloroplasts (‘grana’ means grains). Cell walls
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squamous (flattened) epithelium. are also clearly visible (animal cells lack cell walls).
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1 Cell structure

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is therefore very easy to see when looking down the

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microscope. The deeply staining material in the nucleus KEY WORDS

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is called chromatin (‘chroma’ means colour). Chromatin chromatin: the material of which chromosomes

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is a mass of coiled threads. The threads are seen to
am are made, consisting of DNA, proteins and small

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collect together to form chromosomes during nuclear amounts of RNA; visible as patches or fibres
division (Chapter 5, Section 5.2, Chromosomes). within the nucleus when stained
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Chromatin contains DNA (deoxyribonucleic acid), the

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chromosome: in the nucleus of the cells of

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molecule which contains the instructions (genes) that
eukaryotes, a structure made of tightly coiled
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control the activities of the cell (Chapter 6).

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chromatin (DNA, proteins and RNA) visible during
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Inside the nucleus an even more deeply staining area cell division; the term ‘circular DNA’ is now also

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is visible, the nucleolus. This is made of loops of DNA commonly used for the circular strand of DNA
from several chromosomes. The number of nucleoli is
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present in a prokaryotic cell
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variable, one to five being common in mammals. One of

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nucleolus: a small structure, one or more of
the main functions of nucleoli is to make ribosomes.

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which is found inside the nucleus; the nucleolus

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is usually visible as a densely stained body; its

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Cytoplasm

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function is to manufacture ribosomes using the
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All the living material inside the cell is called protoplasm. information in its own DNA

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It is also useful to have a term for all the living material

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protoplasm: all the living material inside a cell
id

outside the nucleus; it is called cytoplasm. Therefore,

(cytoplasm plus nucleus)

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cytoplasm + nucleus = protoplasm.

cytoplasm: the contents of a cell, excluding
am

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Cytoplasm is an aqueous (watery) material, varying the nucleus
from a fluid to a jelly-like consistency. Using a light
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mitochondrion (plural: mitochondria): the

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microscope, many small structures can be seen within

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it. These have been likened to small organs and are organelle in eukaryotes in which aerobic
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respiration takes place

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therefore known as organelles (meaning ‘little organs’).

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An organelle can be defined as a functionally and cell wall: a wall surrounding prokaryote, plant
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structurally distinct part of a cell. Organelles are often, and fungal cells; the wall contains a strengthening
but not always, surrounded by one or two membranes material which protects the cell from mechanical
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so that their activities can be separated from the damage, supports it and prevents it from bursting
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surrounding cytoplasm. Organising cell activities in by osmosis if the cell is surrounded by a solution
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separate compartments is essential for a structure as with a higher water potential

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complex as an animal or plant cell to work efficiently.

C
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Differences between
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Mitochondria (singular: mitochondrion)

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The most numerous organelles seen with the light

animal and plant cells
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microscope are usually mitochondria (singular:

am

mitochondrion). Mitochondria are only just visible using

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One of the structures commonly found in animal cells

a light microscope. Videos of living cells, taken with the which is absent from plant cells is the centriole. Plant
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aid of a light microscope, have shown that mitochondria cells also differ from animal cells in possessing cell walls,
s

can move about, change shape and divide. They are

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large permanent vacuoles and chloroplasts.

specialised to carry out aerobic respiration.
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Centrioles
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Golgi apparatus Under the light microscope the centriole appears as

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The use of special stains containing silver resulted in the a small structure close to the nucleus (Figure 1.4).
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Golgi apparatus being discovered in 1898 by Camillo Centrioles are discussed later in this chapter.
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Golgi. The Golgi apparatus collects and processes

Cell walls and plasmodesmata
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molecules within the cell, particularly proteins.

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With a light microscope, individual plant cells are more

R

easily seen than animal cells. This is because they are

Note: you do not need to learn this structure. It is
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usually larger and, unlike animal cells, are surrounded

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sometimes called the Golgi body or Golgi complex.

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by a cell wall. Note that the cell wall is an extra

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structure which is outside the cell surface membrane. of the plant, mainly in the leaves. They are relatively

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The wall is relatively rigid because it contains fibres large organelles and so are easily seen with a light

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of cellulose, a polysaccharide which strengthens the microscope. It is even possible to see tiny ‘grains’ or

ev
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wall. The cell wall gives the cell a definite shape. It
am grana (singular: granum) inside the chloroplasts using

-R
prevents the cell from bursting when water enters by a light microscope (Figure 1.7). These are the parts
osmosis, allowing large pressures to develop inside the of the chloroplast that contain chlorophyll, the green
-C

cell (Chapter 4, Section 4.5, Movement of substances pigment which absorbs light during the process of

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across membranes). Cell walls may be reinforced with photosynthesis. Chloroplasts are discussed further in
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extra cellulose or with a hard material called lignin Chapter 13 (Section 13.2, Structure and function of

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for extra strength (Chapter 7). Cell walls are freely chloroplasts).
permeable, allowing free movement of molecules and

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ions through to the cell surface membrane.

KEY WORDS
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Plant cells are linked to neighbouring cells by means

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of pores containing fine strands of cytoplasm. plasmodesma (plural: plasmodesmata): a

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ev

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These structures are called plasmodesmata (singular: pore-like structure found in plant cell walls;
R

plasmodesmata of neighbouring plant cells line

U

plasmodesma). They are lined with the cell surface

C
membrane. Movement through the pores is thought to up to form tube-like pores through the cell walls,
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be controlled by the structure of the pores. allowing the controlled passage of materials from

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one cell to the other; the pores contain ER and

are lined with the cell surface membrane

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Vacuoles
am

Vacuoles are sac-like structures which are surrounded

-R vacuole: an organelle found in eukaryotic cells;
by a single membrane. Although animal cells may a large, permanent central vacuole is a typical
-C

possess small vacuoles such as phagocytic vacuoles feature of plant cells, where it has a variety of
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(Chapter 4, Section 4.5, Movement of substances functions, including storage of biochemicals such
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across membranes), which are temporary structures, as salts, sugars and waste products; temporary
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mature plant cells often possess a large, permanent, vacuoles, such as phagocytic vacuoles (also
central vacuole. The plant vacuole is surrounded by known as phagocytic vesicles), may form in
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a membrane, the tonoplast, which controls exchange animal cells

rs
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between the vacuole and the cytoplasm. The fluid

tonoplast: the partially permeable membrane
ie

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in the vacuole is a solution of pigments, enzymes,

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that surrounds plant vacuoles
ev

sugars and other organic compounds (including some

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waste products), mineral salts, oxygen and carbon chloroplast: an organelle, bounded by an
R

dioxide. envelope (i.e. two membranes), in which

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In plants, vacuoles help to regulate the osmotic photosynthesis takes place in eukaryotes
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properties of cells (the flow of water inwards and photosynthesis: the production of organic
ev
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outwards) as well as having a wide range of other substances from inorganic ones, using energy
functions. For example, the pigments which colour
am

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from light
the petals of certain flowers and the parts of some
vegetables, such as the red pigment of beetroots, may grana (singular: granum): stacks of membranes
-C

be found in vacuoles. inside a chloroplast

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Chloroplasts
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Chloroplasts are organelles specialised for the process

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of photosynthesis. They are found in the green parts

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1 Cell structure

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IMPORTANT

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• You can think of a plant cell as being very similar to an animal cell but with extra structures.

ev
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• Plant cells are often larger than animal cells, although cell size varies enormously.
am

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• Do not confuse the cell wall with the cell surface membrane. Cell walls are relatively thick and physically
-C

strong, whereas cell surface membranes are very thin. Cell walls are freely permeable, whereas cell

s
surface membranes are partially permeable. All cells have a cell surface membrane, but animal cells do

es
not have a cell wall.
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• Vacuoles are not confined to plant cells; animal cells may have small vacuoles, such as phagocytic
vacuoles, although these are not usually permanent structures.

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PRACTICAL ACTIVITY 1.1
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Making temporary slides black and will also colour nuclei and cell walls a pale

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yellow. A dilute solution of methylene blue can be
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A common method of examining material with a light

w
used to stain animal cells such as cheek cells.
microscope is to cut thin slices of the material called

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‘sections’. The advantage of cutting sections is that Viewing specimens yourself with a microscope will

ev
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they are thin enough to allow light to pass through help you to understand and remember structures.
am

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the section. The section is laid (‘mounted’) on a glass Your understanding can be reinforced by making
slide and covered with a coverslip to protect it. Light a pencil drawing on good quality plain paper.
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passing through the section produces an image Remember always to draw what you see, and not
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which can then be magnified using the objective and what you think you should see.
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eyepiece lenses of the microscope.

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Procedure
Biological material may be examined live or in a
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preserved state. Prepared slides contain material that Place the biological specimen on a clean glass slide
rs

and add one or two drops of stain. Carefully lower a

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has been killed and preserved in a life-like condition.

cover over the specimen to protect the microscope
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Temporary slides are quicker and easier to prepare

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lens and to help prevent the specimen from drying
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and are often used to examine fresh material out. Adding a drop of glycerine and mixing it with
R

containing living cells. In both cases the sections the stain can also help prevent drying out.
C

are typically stained before being mounted on the

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• Suitable animal material: human cheek cells

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glass slide.
obtained by gently scraping the lining of the
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Temporary preparations of fresh material are useful cheek with a finger nail
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for quick preliminary investigations. Sometimes

• Suitable plant material: onion epidermal cells,
am

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macerated (chopped up) material can be used,

lettuce epidermal cells, Chlorella cells, moss
as when examining the structure of wood (xylem).
slip leaves
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A number of temporary stains are commonly used.

s
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For example, iodine in potassium iodide solution (See Practical Investigation 1.1 in the Practical
y

is useful for plant specimens. It stains starch blue- Workbook for additional information.)
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PRACTICAL ACTIVITY 1.2

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Biological drawing sections of Practical Activity 7.1 before answering
am the question below, which is relevant to this chapter.

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To reinforce your learning, you will find it useful to
Figures 1.8a and b show examples of good drawing
make labelled drawings of some of your temporary
and labelling technique based on Figures 1.6
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and permanent slides, as well as labelled drawings

s
and 1.7. Note that it is acceptable to draw only

es
of photomicrographs.
a representative portion of the cell contents of
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Practical Activity 7.1 in Chapter 7 provides general Figure 1.7, but add a label explaining this.
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guidance on biological drawing. Read the relevant

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cytoplasm
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nucleus

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chromatin
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small structures (organelles?)

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visible (not all drawn)

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Question
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2 A student was asked to make a high-power drawing

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of three neighbouring cells from Figure 1.6.

Figure 1.9 shows the drawing made by the student.
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Using Practical Activity 7.1 to help you, suggest how

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b
the drawing in Figure 1.9 could be improved.
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cytoplasm nucl
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representative
chloroplast
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portion of
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cytoplasm cytoplasm
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drawn grana visible?

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cell wall
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Figure 1.8: Examples of good drawing technique: a high-power

drawing of three neighbouring animal cells from Figure 1.6;
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b high-power drawing of two neighbouring plant cells from Figure 1.9: A student’s high-power drawing of
ev

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Figure 1.7. three neighbouring cells from Figure 1.6.

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(See Practical Investigation 1.1 in the Practical Workbook for additional information.)
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1 Cell structure

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1.4 Measuring size and Measuring cell size

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Cells and organelles can be measured with a microscope

ev
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calculating magnification
am by means of an eyepiece graticule. This is a transparent

-R
scale. It usually has 100 divisions (see Figure 1.10a).
Magnification is the number of times larger an image of The eyepiece graticule is placed in the microscope
an object is than the real size of the object.
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eyepiece so that it can be seen at the same time as

s
observed size of the image

es
the object to be measured, as shown in Figure 1.10b.
magnification =
Figure 1.10b shows the scale over one of a group of
y

actual size

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or six human cheek epithelial cells (like those shown in

I Figure 1.6). The cell selected lies between 40 and 60 on

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M = the scale. We therefore say it measures 20 eyepiece units

A

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M = magnification in diameter (the difference between 60 and 40). We will

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not know the actual size of the eyepiece units until the
I = observed size of the image (what you can measure

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eyepiece graticule is calibrated.

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with a ruler)
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A = actual size (the real size – for example, the size of a KEY WORDS

C
cell before it is magnified).
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If you know two of the values M, I and A, you can work magnification: the number of times larger an

ie
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out the third one. For example, if the observed size of image of an object is than the real size of the

ev
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the image and the magnification are known, you can object; magnification = image size ÷ actual (real)
I size of the object
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work out the actual size A = . If you write the formula

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M eyepiece graticule: small scale that is placed in a
in a triangle as shown below and cover up the value you
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microscope eyepiece
s

want to find, it should be obvious how to do the right

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calculation.
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I
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M × A
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a cheek cells on a slide b eyepiece graticule c

scale (arbitrary
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on the stage of the

id

microscope units)
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0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100
0 10 20 30 40 50 60 70 80 90 100
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0 0.1 0.2
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eyepiece
graticule in
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the eyepiece
stage micrometer
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of the
scale (marked in
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microscope
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0.01 mm and 0.1 mm

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divisions)
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Figure 1.10: Microscopical measurement. Three fields of view seen using a high-power (×40) objective lens: a an eyepiece
C

graticule scale; b superimposed images of human cheek epithelial cells and the eyepiece graticule scale; c superimposed
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images of the eyepiece graticule scale and the stage micrometer scale.
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To calibrate the eyepiece graticule, a miniature

w
a
transparent ruler called a stage micrometer is placed on

ie
id
the microscope stage and is brought into focus. This

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scale may be etched onto a glass slide or printed on a
am

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transparent film. It commonly has subdivisions of 0.1
and 0.01 mm. The images of the stage micrometer and
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the eyepiece graticule can then be superimposed (placed

s
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on top of one another) as shown in Figure 1.10c.
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Calculating magnification

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Figure 1.11 shows micrographs of two sections through

ie

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the same plant cell. The difference in appearance of the

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two micrographs is explained in the next section.

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If we know the actual (real) length of a cell in such a

R

C
micrograph, we can calculate its magnification, M, using b
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the formula:

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id

I
M =

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A
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epidermal cell
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cell wall
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KEY WORDS
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chloroplast
stage micrometer: very small, accurately drawn
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starch grain
Pr

P
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scale of known dimensions, engraved on a

microscope slide vacuole
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nucleus
micrograph: a picture taken with the aid of a
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microscope; a photomicrograph (or light mitochondrion

ie

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micrograph) is taken using a light microscope; cytoplasm

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an electron micrograph is taken using an

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electron microscope
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Figure 1.11: Micrographs of two sections of the same

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plant cells, as seen a with a light microscope, and b with

ie

an electron microscope. Both are shown at the same

id

magnification (about ×750).

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am

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WORKED EXAMPLE
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1 In the eyepiece graticule shown in Figure 1.10, The diameter of the cell shown superimposed
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100 units measure 0.25 mm. Hence, the value of on the scale in Figure 1.8b measures 20 eyepiece
each eyepiece unit is: units and so its actual diameter is:
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0.25
= 0.0025 mm 20 × 2.5 μm = 50 μm
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100
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This diameter is greater than that of many human

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Or, converting mm to μm:

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cells because the cell is a flattened epithelial cell.

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0. 25 1000
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2. 5 µm
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100
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1 Cell structure

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WORKED EXAMPLE

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2 Suppose we want to know the magnification of the Step 3 Use the equation to calculate the

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plant cell labelled P in Figure 1.11b. The real length
am magnification.

-R
of the cell is 80 μm.
image size, l
-C

magnification, M =

s
Step 1 Measure the length in mm of the cell in the actual size, A

es
micrograph using a ruler. You should find
50 000 µm
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that it is about 50 mm. =

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80 µm
Step 2 Convert mm to μm. (It is easier if we first

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= × 625
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convert all measurements to the same

rs
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units – in this case micrometres, μm.) The multiplication sign (×) in front of the number
ie

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625 means ‘times’. We say that the magnification

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So: 1 mm = 1000 µm is ‘times 625’.

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50 mm = 50 × 1000 µm
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C
= 50 000 µm
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Question
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3 a Calculate the magnification of the drawing of b Calculate the actual (real) length of the
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the animal cell in Figure 1.4. chloroplast labelled X in Figure 1.34.

s
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WORKED EXAMPLE
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3 Figure 1.12 shows a lymphocyte with a scale Step 1 Measure the scale bar. Here, it is 36 mm.
rs
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bar. We can use this scale bar to calculate the Step 2 Convert mm to μm:
ie

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magnification.
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36 mm = 36 × 1000 μm = 36 000 μm
ev

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Step 3 The scale bar represents 6 µm. This is the

R

actual size, A. Use the equation to calculate the

C
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magnification:
w
ie

image size, l
id

magnification, M =
ev
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actualsize, A
am

36 000µm
-R

=
6µm
-C

= × 6000
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6 µm
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Figure 1.12: A lymphocyte.

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Calculating the real size of an separate points. If the two points cannot be resolved,

w
they will be seen as one point. In practice, resolution is

ie
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object from its magnification the amount of detail that can be seen – the greater the

ev
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am resolution, the greater the detail.
To calculate the real or actual size of an object, we can

-R
use the same magnification equation. The maximum resolution of a light microscope is 200 nm.
The reason for this is explained in the next section, ‘The
-C

s
electromagnetic spectrum’. A resolution of 200 nm means

es
WORKED EXAMPLE that, if two points or objects are closer together than
y

Pr
200 nm, they cannot be distinguished as separate.
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4 Figure 1.20 shows parts of three plant cells You might imagine that you could see more detail in

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magnified ×5600. Suppose we want to know the Figure 1.11a by magnifying it (simply making it larger).
actual length of the labelled chloroplast in this
rs
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In practice you would be able to see what is already

electron micrograph.
ie

there more easily, but you would not see any more
ve

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detail. The image would just get more and more blurred
ev

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Step 1 Measure the observed length of the
as magnification increased. The resolution would not
image of the chloroplast (I), in mm,
R

be greater.

C
using a ruler. The maximum length is
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25 mm.
The electromagnetic spectrum

ie
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Step 2 Convert mm to μm:

ev
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25 mm = 25 × 1000 μm = 25 000 μm How is resolution linked with the nature of light? One
am

-R of the properties of light is that it travels in waves. The

Step 3 Use the equation to calculate the lengths of the waves of visible light vary, ranging from
-C

actual length: about 400 nm to about 700 nm. The human eye can
s
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distinguish between these different wavelengths, and

image size, l
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actual size, A = in the brain the differences are converted to colour

Pr
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magnification, M differences. Waves that are 400 nm in length are seen as

25 000 µm violet. Waves that are 700 nm in length are seen
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=
5600 as red.
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= 4.5 µm (to one Visible light is a form of electromagnetic radiation.

ie

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decimal place) The range of different wavelengths of electromagnetic

y
ev

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radiation is called the electromagnetic spectrum. Visible

R

light is only one part of this spectrum. Figure 1.13

C

shows some of the parts of the electromagnetic

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1.5 Electron microscopy

w

spectrum. The longer the waves, the lower their

ie
id

frequency. (All the waves travel at the same speed, so

Before studying what cells look like with an electron
ev

imagine them passing a post: shorter waves pass at

br

microscope, you need to understand the difference higher frequency.) In theory, there is no limit to how
am

-R

between magnification and resolution. short or how long the waves can be. Wavelength changes
with energy: the greater the energy, the shorter the
-C

wavelength.
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Magnification and resolution

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KEY WORD
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Look again at Figure 1.11. Figure 1.11a is a light

micrograph. Figure 1.11b is an electron micrograph.
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Both micrographs are of the same cells and both have resolution: the ability to distinguish between
two objects very close together; the higher the
rs
w

the same magnification. However, you can see that

resolution of an image, the greater the detail that
ie

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Figure 1.11b, the electron micrograph, is much clearer.

can be seen
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This is because it has greater resolution. Resolution

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can be defined as the ability to distinguish between two

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X-rays infrared

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microwaves

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gamma rays UV radio and TV waves
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5 7 9 11 13
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0.1 nm 10 nm 1000 nm 10 nm 10 nm 10 nm 10 nm 10 nm

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visible light

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400 nm 500 nm 600 nm 700 nm

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violet green orange red

ie

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Figure 1.13: Diagram of the electromagnetic spectrum. The numbers indicate the wavelengths of the different types of

y
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electromagnetic radiation. Note the waves vary from very short to very long. Visible light is part of the spectrum. The double-
R

headed arrow labelled UV is ultraviolet light.

C
ge

w
ie
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wavelength stained mitochondrion The general rule when viewing specimens is that the

ev
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400 nm of diameter 1000 nm limit of resolution is about one half the wavelength
interferes with light waves
am

of the radiation used to view the specimen. In other

-R
words, if an object is any smaller than half the
-C

wavelength of the radiation used to view it, it cannot

s

be seen separately from nearby objects. This means

es

that the best resolution that can be obtained using a

y

Pr
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microscope that uses visible light (a light microscope)

is 200 nm, since the shortest wavelength of visible light
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is 400 nm (violet light). Ribosomes are approximately

rs
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25 nm in diameter and can therefore never be seen

ie

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using a light microscope.

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If an object is transparent, it will allow light waves to

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pass through it and therefore will still not be visible. This

R

is why many biological structures have to be stained

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before they can be seen.

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Question
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stained ribosomes of diameter 25 nm 4 Explain why ribosomes are not visible using a light
-C

do not interfere with light waves microscope.

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Figure 1.14: A mitochondrion and some ribosomes in the

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The electron microscope

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path of light waves of 400 nm length.

So how can we look at things smaller than 200 nm?
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Now look at Figure 1.14. It shows a mitochondrion The only solution to this problem is to use radiation
rs
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and some very small cell organelles called ribosomes. of a shorter wavelength than visible light. If you study
ie

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It also shows some wavy blue lines that represent light Figure 1.13, you will see that ultraviolet light or X-rays
y
ev

look like possible candidates. A much better solution,

op
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of 400 nm wavelength. This is the shortest visible

though, is to use electrons. Electrons are negatively
R

wavelength. The mitochondrion is large enough to

U

interfere with the light waves. However, the ribosomes charged particles which orbit the nucleus of an atom.
e

When a metal becomes very hot, some of its electrons

w

are far too small to have any effect on the light waves.
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gain so much energy that they escape from their orbits,
Viewing specimens with the

w
similar to a rocket escaping from Earth’s gravity. Free

ie
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electrons behave like electromagnetic radiation. They electron microscope

ev
br
have a very short wavelength: the greater the energy,
am

-R
the shorter the wavelength. Electrons are a very suitable Figure 1.16 shows how a TEM works and Figure 1.17
form of radiation for microscopy for two major reasons. shows one in use.
-C

First, their wavelength is extremely short (at least as

s
es
short as that of X-rays). Second, unlike X-rays, they are electron gun and anode –
y

negatively charged, so they can be focused easily using produce a beam of electrons

Pr
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electromagnets (a magnet can be made to alter the path of

the beam, the equivalent of a glass lens bending light).

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electron beam
Using an electron microscope, a resolution of 0.5 nm can

rs
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vacuum
be obtained, 400 times better than a light microscope.
ie

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pathway of electrons

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Transmission and scanning

R

C
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condenser electromagnetic
electron microscopes

w
lens – directs the electron beam

ie
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Two types of electron microscope are now in common onto the specimen

ev
br

use. The transmission electron microscope (TEM) was

am

the type originally developed. The beam of electrons is

-R
passed through the specimen before being viewed. Only specimen is placed on a
-C

those electrons that are transmitted (pass through the

s

grid
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specimen) are seen. This allows us to see thin sections of

y

specimens, and thus to see inside cells. In the scanning

Pr
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electron microscope (SEM), the electron beam is used

objective electromagnetic
to scan the surfaces of structures and only the reflected
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lens – produces an image

beam is observed.
rs
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An example of a scanning electron micrograph is shown

ie

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in Figure 1.15. The advantage of this microscope is that

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surface structures can be seen. Because much of the projector electromagnetic

R

specimen is in focus at the same time, a three-dimensional lenses – focus the magnified
C

appearance is achieved. A disadvantage of the SEM is image onto the screen

ge

that it cannot achieve the same resolution as a TEM.

ie
id

Using an SEM, resolution is between 3 nm and 20 nm.

ev
br
am

screen or photographic film

-R

or sensor – shows the image

of the specimen
-C

s
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Figure 1.16: How a TEM works.

op

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Note: the structure of an electron microscope is

rs
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extension content, and is not part of the syllabus.

ie

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y
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Figure 1.15: Scanning electron micrograph (SEM) of a

op
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tardigrade. Tardigrades or water bears, are about 0.5 mm It is not possible to see an electron beam, so to make
R

the image visible the electron beam has to be projected

C

long, with four pairs of legs. They are common in soil and
onto a fluorescent screen. The areas hit by electrons
e

can survive extreme environmental conditions (×86).

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1 Cell structure

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The electron beam, and therefore the specimen and

w
the fluorescent screen, must be in a vacuum. If the

ie
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electrons collided with air molecules, they would scatter,

ev
br
am making it impossible to achieve a sharp picture. Also,

-R
water boils at room temperature in a vacuum, so all
specimens must be dehydrated before being placed in
-C

the microscope. This means that only dead material or

s
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non-living can be examined. Great efforts are therefore
y

made to try to preserve material in a life-like state when

Pr
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preparing it for electron microscopy.

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1.6 Plant and animal cells

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ev

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as seen with an electron

R

C
microscope
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Figure 1.17: A TEM in use.

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ie
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The fine (detailed) structure of a cell as revealed by the

ev
br

shine brightly, giving overall a black and white picture. electron microscope is called ultrastructure and is shown
The stains used to improve the contrast of biological
am

-Rin Figures 1.18–1.21.

specimens for electron microscopy contain heavy metal
atoms, which stop the passage of electrons. The resulting
-C

picture is like an X-ray photograph, with the more

es

densely stained parts of the specimen appearing blacker.

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Pr

‘False-colour’ images can be created by colouring the

op

standard black and white image using a computer.

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Question
rs
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5 Copy and complete Table 1.2, which compares light microscopes with electron microscopes. Some boxes have been
y
ev

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filled in for you.

R

Feature Light microscope Electron microscope

ge

source of radiation
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id

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br

wavelength of radiation used about 0.005 nm

am

-R

maximum resolution 0.5 nm in practice

-C

lenses glass
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specimen non-living or dead

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stains coloured dyes

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image coloured
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Table 1.2: Comparison of light microscopes and electron microscopes.

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Golgi apparatus

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cell surface
ie

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membrane

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lysosome

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boundary between
mitochondria the two cells
-C

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nucleolus
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y
ev

endoplasmic
op
ni
R

reticulum
U

nucleus
ge

w
ie
id

glycogen granules
ev
br
am

-R

microvillus
chromatin
-C

s
es
y

Pr
op

nuclear envelope
ity
C

ribosomes
rs
w
ie

ve

y
ev

op
ni

Figure 1.18: Parts of two representative animal cells as seen with a TEM. The cells are liver cells from a rat (×9600). The
R

nucleus is clearly visible in one of the cells. The boundary between the two cells is difficult to see because the cell surface
e

membranes are so thin.

g

ie
id

ev
br
am

-R

18
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1 Cell structure

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ge
cell surface membrane microvilli

w
ie
id
Golgi vesicle

ev
br
centrosome with two centrioles close to the
am

-R
nucleus and at right angles to each other Golgi apparatus
-C

s
nuclear envelope microtubules radiating

es
(two membranes) from centrosome
y

Pr
op

nucleolus
nucleus

ity
C

chromatin ribosomes

rs
w
ie

ve
nuclear pore

y
ev

lysosome

op
ni
R

C
rough endoplasmic reticulum
ge

smooth endoplasmic reticulum

w
ie
id

cytoplasm

ev
br

mitochondrion
am

-R
Figure 1.19: Ultrastructure of a typical animal cell as seen with an electron microscope. This drawing is based on many
micrographs of animal cells. In reality, the endoplasmic reticulum is more extensive than shown here, and free ribosomes may
-C

be more extensive. Glycogen granules are sometimes present in the cytoplasm.

es
y

Pr

Question
op

ity
C

6 Compare Figure 1.19 with Figure 1.4. Name the structures in an animal cell that can be seen with the electron
microscope but not with the light microscope.
rs
w
ie

ve

cell surface ribosome

y
ev

membrane
op
ni

vacuole
R

nuclear envelope tonoplast

ge

chromatin
w
ie
id

ev
br

nucleolus chloroplast
am

-R

nuclear pore
cell wall
endoplasmic
-C

reticulum
es

mitochondrion
y

Pr
op

starch grain
Golgi apparatus
ity
C

rs
w
ie

ve

y
ev

op
ni
R

Figure 1.20: Representative plant cells as seen with a TEM. The cells are palisade cells from a soya bean leaf. The boundaries
e

w
g

between the cells can clearly be seen due to the presence of cell walls (×5600).
ie
id

ev
br
am

-R

19
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ni
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C
ge
Question

w
ie
id
7 Compare Figure 1.21 with Figure 1.5. Name the structures in a plant cell that can be seen with the electron

ev
br
microscope but not with the light microscope.
am

-R
-C

s
es
middle lamella chloroplast
y

cytoplasm

Pr
plasmodesma
op

Golgi apparatus

ity
C

Golgi vesicle

rs
w

cell walls of neighbouring cells

ie

ve

y
tonoplast
ev

op
ni
vacuole
cell sap
R

C
ge

mitochondrion

w
ie
id

smooth ER

ev
br
am

-R
cell surface membrane
(pressed against cell wall)
-C

s
es
y

ribosomes
Pr
op

ity
C

nuclear pore
rs
w
ie

ve

nucleolus envelope grana

y
ev

op
ni

nucleus chromatin chloroplast

R

nuclear envelope
ge

(two membranes) rough ER microtubule

ie
id

Figure 1.21: Ultrastructure of a typical plant cell as seen with the electron microscope. This drawing is based on many
ev
br

micrographs of plant cells. In reality, the ER is more extensive than shown. Free ribosomes may also be more extensive.
am

-R
-C

Cell surface membrane cell surface membrane appears

es

as two dark lines (shown by the

label lines) with a pale interior
y

The cell surface membrane is extremely thin (about

Pr
op

7 nm). However, at very high magnifications it can be

seen to have three layers – two dark (heavily stained) outside of cell
ity
C

layers surrounding a narrow, pale interior (Figure 1.22).

rs
w

The membrane is partially permeable and controls inside of cell (cytoplasm)

ie

ve

exchange between the cell and its environment.

y
ev

Membrane structure is discussed further in Chapter 4.

op
ni

Figure 1.22: Cell surface membrane (×250 000). At this

R

magnification the membrane appears as two dark lines at

e

the edge of the cell.

w
g

ie
id

ev
br
am

-R

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1 Cell structure

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ge
Microvilli Question

w
ie
id
Microvilli (singular: microvillus) are finger-like extensions 8 a Using the magnification given, determine

ev
br
of the cell surface membrane. They are typical of certain
am the actual maximum diameter of the nucleus

-R
animal cells, such as epithelial cells. Epithelial cells cover shown in Figure 1.23.
the surfaces of structures. The microvilli greatly increase b The diameter you have calculated for the
-C

the surface area of the cell surface membrane, as shown in

s
nucleus shown in Figure 1.23 is not necessarily

es
Figure 1.19. This is useful, for example, for reabsorption the maximum diameter of this nucleus. Explain
in the proximal convoluted tubules of the kidney and for
y

why this is the case.

Pr
op

absorption of digested food into cells lining the gut.

ity
C

IMPORTANT
KEY WORDS
rs
w

Use modelling clay to make a spherical shape

ie

ve
microvilli (singular: microvillus): small, finger-like (a ball), like a nucleus. Try cutting it into two at

y
ev

op
ni
extensions of a cell which increase the surface different places and looking at the sizes of the cut
R

area of the cell for more efficient absorption surfaces. This represents the process of sectioning
U

C
or secretion material for examination using a microscope.
ge

w
ie
id

Nucleus
ev
br
am

-R
The nucleus (Figure 1.23) is the largest cell organelle.
mitochondrion
-C

s
es
y

endoplasmic
Pr
op

reticulum
ity
C

rs
w
ie

ve

nuclear pore
y
ev

op
ni

nuclear envelope
R

nucleolus
ge

nucleus
ie
id

ev
br
am

-R
-C

chromatin
es
y

Pr
op

ity
C

rs
w

Figure 1.23: Transmission electron micrograph (TEM) of a nucleus. This is the nucleus of a cell from the pancreas of a bat
ie

ve

(×11000). The circular nucleus is surrounded by a double-layered nuclear envelope containing nuclear pores. The nucleolus is
y
ev

op
ni

more darkly stained. Rough ER is visible in the surrounding cytoplasm.

R

C
e

w
g

ie
id

ev
br
am

-R

21
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ge
The nuclear envelope when, as during nuclear division, ribosome synthesis

w
ceases. The nucleolus as a structure then disappears.

ie
id
The nucleus is surrounded by two membranes, forming

ev
the nuclear envelope. The outer membrane of the nuclear

br
envelope is continuous with the endoplasmic reticulum
am Endoplasmic reticulum

-R
(Figures 1.19 and 1.21).
When cells were first seen with the electron microscope,
-C

The nuclear envelope has many small pores called biologists were amazed to see so much detailed structure.

s
es
nuclear pores. These allow and control exchange between The existence of much of this had not been suspected.
the nucleus and the cytoplasm. Examples of substances
y

This was particularly true of the endoplasmic reticulum

Pr
op

leaving the nucleus through the pores are messenger (ER) (Figures 1.23, 1.24 and 1.28). The membranes of
RNA (mRNA), transfer RNA (tRNA) and ribosomes the ER form flattened compartments called sacs or

ity
C

for protein synthesis. Examples of substances entering

rs
w

through the nuclear pores are proteins (to help make

ie

ve
ribosomes), nucleotides, ATP (adenosine triphosphate)

y
ev

and some hormones such as thyroid hormone T3.

op
ni
R

Chromosomes and chromatin

C
ge

The nucleus contains the chromosomes. Chromosomes

w
contain DNA, the genetic material. DNA is organised

ie
id

into functional units called genes. Genes control the

ev
br

activities of the cell and inheritance; thus the nucleus

am

controls the cell’s activities.

-R
rough ER
The DNA molecules are so long (a human cell contains
-C

about two metres of DNA) that they have to be folded

es

up into a more compact shape to prevent the strands

y

Pr

becoming tangled. This is achieved by combining with free

op

proteins, particularly with proteins known as histones. ribosomes

ity
C

The combination of DNA and proteins is known as

chromatin. Chromatin also contains some RNA. Thus,
rs
w

chromosomes are made of chromatin (Chapter 5,

ie

ve

Section 5.2, Chromosomes).

y
ev

Figure 1.24: TEM of rough ER covered with ribosomes

op
ni

When a cell is about to divide, the nucleus divides first so that (black dots) (×17 000). Some free ribosomes can also be
R

each new cell will have its own nucleus (Chapters 5 and 16). seen in the cytoplasm on the left.
ge

Also within the nucleusis a structure called the nucleolus.

ie
id

Nucleolus KEY WORDS

ev
br

The nucleolus appears as a darkly stained, rounded nuclear envelope: the two membranes, situated
am

-R

structure in the nucleus (Figure 1.23). As mentioned close together, that surround the nucleus; the
earlier, one or more may be present, although one is most envelope is perforated with nuclear pores
-C

common. Its function is to make ribosomes using the

es

information in its own DNA. It contains a core of DNA nuclear pores: pores found in the nuclear envelope
y

which control the exchange of materials, e.g.

Pr

from one or more chromosomes which contain the genes

op

that code for ribosomal RNA (rRNA), the form of RNA mRNA, between the nucleus and the cytoplasm
ity
C

used in the manufacture of ribosomes. It also contains endoplasmic reticulum (ER): a network of
genes for making tRNA. Around the core are less dense
rs
w

flattened sacs running through the cytoplasm of

regions where the ribosomal subunits are assembled, eukaryotic cells; molecules, particularly proteins,
ie

ve

combining the rRNA with ribosomal proteins imported

y

can be transported through the cell inside the

ev

op
ni

from the cytoplasm. The more ribosomes a cell makes, sacs separate from the rest of the cytoplasm; ER
R

the larger its nucleolus. is continuous with the outer membrane of the
C

nuclear envelope
e

The different parts of the nucleolus only come together

w
g

during the manufacture of ribosomes. They separate

ie
id

ev
br
am

-R

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1 Cell structure

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ge
cisternae. Processes can take place inside the cisternae mRNA, tRNA, amino acids and regulatory proteins,

w
separated from the cytoplasm. Molecules, particularly to gather together in one place (Chapter 6, Section 6.5,

ie
id
proteins, can be transported through the ER separate Protein synthesis).

ev
br
from the rest of the cytoplasm. The ER is continuous
am

-R
with the outer membrane of the nuclear envelope
(Figures 1.19 and 1.21).
-C

s
es
Rough endoplasmic reticulum
y

Pr
There are two types of ER: rough ER (RER) and
op

smooth ER (SER). RER is so called because it is

ity
C

covered with many tiny organelles called ribosomes

rs
(described later). These are just visible as black dots
w

in Figures 1.23 and 1.24. Ribosomes are the sites of

ie

ve

y
protein synthesis (Chapter 6). They can be found free in
ev

op
ni

the cytoplasm as well as on the RER.

R

C
ge

w
Smooth endoplasmic reticulum

ie
id

SER has a smooth appearance because it lacks Figure 1.25: Structure of the human 80S ribosome.

ev
br

ribosomes. It has a completely different function to

am

RER. It makes lipids and steroids, such as cholesterol

-R
and the reproductive hormones oestrogen and
Golgi apparatus
-C

testosterone. SER is also a major storage site for calcium

s
es

ions. This explains why it is abundant in muscle cells,

The Golgi apparatus is a stack of flattened sacs called
where calcium ions are involved in muscle contraction
y

Pr

cisternae (Figure 1.26). More than one Golgi apparatus

op

(Chapter 15, Section 15.3, Muscle contraction). In the

may be present in a cell. The stack is constantly being
liver, SER is involved in drug metabolism.
ity
C

formed at one end from vesicles which bud off from

the ER, and are broken down again at the other end to
rs
w

form Golgi vesicles. The stack of sacs together with the

ie

ve

Ribosomes associated vesicles is referred to as the Golgi apparatus

y
ev

op
ni

or Golgi complex.
Ribosomes are very small and are not visible with a
R

light microscope. At very high magnifications using

KEY WORDS
ge

an electron microscope they can be seen to consist

w

of two subunits: a large and a small subunit. The

ie

ribosome: a tiny organelle found in large

id

sizes of structures this small are often quoted in S

numbers in all cells; prokaryotic ribosomes
ev
br

units (Svedberg units). S units are a measure of how

are about 20 nm in diameter while eukaryotic
am

rapidly substances sediment in a high speed centrifuge

-R

ribosomes are about 25 nm in diameter

(an ultracentrifuge). The faster they sediment, the
-C

higher the S number. Eukaryotic ribosomes are 80S Golgi apparatus (Golgi body, Golgi complex):
s

ribosomes. The ribosomes of prokaryotes are 70S

es

an organelle found in eukaryotic cells; the Golgi

ribosomes, so are slightly smaller. Mitochondria and apparatus consists of a stack of flattened sacs,
y

Pr
op

chloroplasts contain 70S ribosomes, revealing their constantly forming at one end and breaking up
prokaryotic origins (see the sections on mitochondria into Golgi vesicles at the other end
ity
C

and chloroplasts).
Golgi vesicles: carry their contents to other parts
rs
w

Ribosomes are made of roughly equal amounts by of the cell, often to the cell surface membrane
ie

ve

mass of ribosomal RNA (rRNA) and protein. Their

y

for secretion; the Golgi apparatus chemically

ev

op
ni

three-dimensional structure has now been worked modifies the molecules it transports, e.g. sugars
R

out (Figure 1.25). Ribosomes allow all the interacting

U

may be added to proteins to make glycoproteins

C

molecules involved in protein synthesis, such as

e

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The Golgi apparatus collects and processes molecules,
Lysosomes

w
particularly proteins from the RER. It contains

ie
id
hundreds of enzymes for this purpose. After processing, Lysosomes are simple sacs, surrounded by a single

ev
br
the molecules can be transported in Golgi vesicles to
am membrane. In animal cells they are usually 0.1–0.5 µm

-R
other parts of the cell or out of the cell. Releasing in diameter (Figure 1.27). In plant cells the large central
molecules from the cell is called secretion and the vacuole may act as a lysosome, although lysosomes
-C

pathway followed by the molecules is called the secretory similar to those in animal cells are also seen in the

s
es
pathway. These are some examples of the functions of cytoplasm.
y

the Golgi apparatus

Pr
op

KEY WORD

ity
C

lysosome: a spherical organelle found in

rs
w

eukaryotic cells; it contains digestive (hydrolytic)

ie

ve
enzymes and has a variety of destructive

y
ev

functions, such as removal of old cell organelles

op
ni
R

C
ge

w
ie
id

ev
br
am

-R
-C

s
es
y

Pr
op

Figure 1.26: TEM of a Golgi apparatus. A central stack of

ity
C

saucer-shaped sacs can be seen budding off small Golgi

rs
w

vesicles (green). These may form secretory vesicles whose

ie

ve

contents can be released at the cell surface by exocytosis

y
ev

(Chapter 4).
op
ni

Figure 1.27: Lysosomes (orange) in a mouse kidney cell

R

(×55 000). They contain cell structures in the process of

U

• Golgi vesicles are used to make lysosomes. digestion. Cytoplasm is coloured blue here.
ge

• Sugars are added to proteins to make molecules

ie
id

known as glycoproteins. Lysosomes contain digestive enzymes. The enzymes

ev
br

are called hydrolases because they carry out hydrolysis

• Sugars are added to lipids to make glycolipids.
am

-R

reactions. These enzymes must be kept separate from

Glycoproteins and glycolipids are important the rest of the cell to prevent damage. Lysosomes are
components of membranes (Chapter 4, Section
-C

responsible for the breakdown (digestion) of unwanted

s

4.2, Structure of membranes) and are important

es

substances and structures such as old organelles or

molecules in cell signalling (Chapter 4, Section 4.4, even whole cells. Hydrolysis works fastest in an acid
y

Pr

Cell signalling).
op

environment so the contents of lysosomes are acidic,

• During plant cell division, Golgi enzymes are pH 4–5 compared with 6.5–7.0 in the surrounding
ity
C

involved in the synthesis of new cell walls. cytoplasm. Among the 60+ enzymes contained in
rs
w

lysosomes are proteases, lipases and nucleases which

• In the gut and the gas exchange system, cells
ie

ve

break down proteins, lipids and nucleic acids respectively.

y

called goblet cells release a substance called mucin

ev

The enzymes are synthesised on RER and delivered to

op
ni

from the Golgi apparatus (Chapter 9, Section 9.4, lysosomes via the Golgi apparatus.
R

Warming and cleaning the air). Mucin is one of the

C

main components of mucus.

e

w
g

ie
id

ev
br
am

-R

24
-C

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ge
The activities of lysosomes can be split into the four

w
categories discussed below. RER

ie
id

ev
br
Getting rid of unwanted cell components
am

-R
Lysosomes can engulf and destroy unwanted cell mitochondrial
components, such as molecules or organelles, that are envelope
-C

s
located inside the cell.

es
y

cristae

Pr
op

Endocytosis matrix
nuclear pore

ity
Endocytosis is described in more detail in
C

Chapter 4 (Section 4.5, Movement of substances across nucleus

rs
w

membranes). Material may be taken into the cell by

ie

ve
endocytosis, for example when white blood cells engulf Figure 1.28: Mitochondrion (orange) with its double

y
ev

bacteria. Lysosomes may fuse with the endocytic membrane (envelope); the inner membrane is folded to

op
ni

vacuoles formed and release their enzymes to digest form cristae (×20 000). Mitochondria are the sites of aerobic
R

C
the contents. cell respiration. Note also the RER.
ge

w
ie
Exocytosis
id

The number of mitochondria in a cell is very variable.

ev
br

Lysosomal enzymes may be released from the cell for As they are responsible for aerobic respiration, it is not
am

extracellular digestion. An example is the replacement

-R
surprising that cells with a high demand for energy,
of cartilage by bone during development. The heads of such as liver and muscle cells, contain large numbers of
-C

sperms contain a special lysosome, the acrosome, for mitochondria. A liver cell may contain as many as 2000
s

digesting a path through the layers of cells surrounding

es

mitochondria. If you exercise regularly, your muscles will

the egg just before fertilisation.
y

make more mitochondria.

Pr
op

Self-digestion Functions of mitochondria and the

ity
C

The contents of lysosomes are sometimes released role of ATP

rs
w

into the cytoplasm. This results in the whole cell being

ie

ve

The main function of mitochondria is to carry out

digested (a process called autolysis). This may be part
y
ev

aerobic respiration, although they do have other

op
ni

of normal development, as when a tadpole tail is

functions, such as the synthesis of lipids. During
R

reabsorbed during metamorphosis or when a uterus is

C

respiration, a series of reactions takes place in which

restored to its normal size after pregnancy. It also occurs
ge

energy is released from energy-rich molecules such as

w

after the death of an individual as membranes lose their

sugars and fats. Most of the energy is transferred to
ie
id

partial permeability.
molecules of ATP (adenosine triphosphate). This is the
ev
br

energy-carrying molecule found in all living cells. It is

am

-R

known as the universal energy carrier.

Mitochondria
-C

Structure KEY WORDS

s
es

The structure of the mitochondrion (plural: cristae (singular: crista): folds of the inner
y

Pr

mitochondria) as seen with the electron microscope is

op

membrane of the mitochondrial envelope on

visible in Figures 1.18, 1.28 and 12.10. Mitochondria which are found stalked particles of ATP synthase
ity
C

are usually about 1 μm in diameter and can be various and electron transport chains associated with
shapes, often sausage-shaped as in Figure 1.28. They
rs
w

aerobic respiration
are surrounded by two membranes (an envelope).
ie

ve

ATP (adenosine triphosphate): the molecule

y

The inner membrane is folded to form finger-like

ev

op
ni

cristae (singular: crista) which project into the interior that is the universal energy currency in all living
R

of the mitochondrion which is called the matrix. cells; the purpose of respiration is to make ATP
C

The space between the two membranes is called the

e

w
g

intermembrane space.
ie
id

ev
br
am

-R

25
-C

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ni
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C
ge
The reactions of respiration take place in solution in the Microtubules are made of a protein called tubulin.

w
matrix and in the inner membrane (cristae). The matrix Tubulin has two forms, α-tubulin (alpha-tubulin) and

ie
id
contains enzymes in solution, including those of the β-tubulin (beta-tubulin). α- and β-tubulin molecules

ev
br
Krebs cycle. Electron carriers are found in the cristae.
am combine to form dimers (double molecules). These

-R
For more detail, see Chapter 12 (Section 12.2). dimers are then joined end to end to form long
‘protofilaments’. This is an example of polymerisation,
Once made, ATP leaves the mitochondrion and, as
-C

the process by which giant molecules are made by

s
it is a small, soluble molecule, it can spread rapidly

es
joining together many identical subunits. Thirteen
to all parts of the cell where energy is needed. Its
y

protofilaments line up alongside each other in a ring to

Pr
energy is released by breaking the molecule down
op

form a cylinder with a hollow centre. This cylinder is

to ADP (adenosine diphosphate). This is a hydrolysis
the microtubule. Figure 1.29a shows the helical pattern

ity
C

reaction. The ADP can then be recycled in a

formed by neighbouring α- and β-tubulin molecules.
mitochondrion for conversion back to ATP during

rs
w

aerobic respiration. Apart from their mechanical function of support,

ie

ve
microtubules have a number of other functions.

y
ev

op
ni

The endosymbiont theory • Secretory vesicles and other organelles and cell
R

C
components can be moved along the outside
ge

Note: The endosymbiont theory is extension surfaces of the microtubules, forming an

w
content, and is not part of the syllabus. intracellular transport system, as in the movement

ie
id

of Golgi vesicles during exocytosis.

ev
br

In the 1960s, it was discovered that mitochondria and • During nuclear division (Chapter 5), a spindle
am

-R
chloroplasts contain ribosomes which are slightly smaller made of microtubules is used for the separation of
than those in the cytoplasm and are the same size as chromatids or chromosomes.
-C

those found in bacteria. Cytoplasmic ribosomes are 80S,

es

while those of bacteria, mitochondria and chloroplasts • Microtubules form part of the structure of
centrioles.
y

are 70S. It was also discovered in the 1960s that

Pr
op

mitochondria and chloroplasts contain small, circular • Microtubules form an essential part of the
ity

DNA molecules, also like those found in bacteria. It was

C

mechanism involved in the beating movements of

later proved that mitochondria and chloroplasts are, in cilia and flagella.
rs
w

effect, ancient bacteria which now live inside the larger

ie

ve

cells of animals and plants (see ‘Thinking outside the The assembly of microtubules from tubulin molecules is
y
ev

box’ at the beginning of this chapter). This is known controlled by special locations in cells called microtubule
op
ni

as the endosymbiont theory. ‘Endo’ means ‘inside’ and organising centres (MTOCs). These are discussed further in
R

a ‘symbiont’ is an organism which lives in a mutually the following section on centrioles. Because of their simple
ge

beneficial relationship with another organism. The DNA construction, microtubules can be formed and broken down
w

and ribosomes of mitochondria and chloroplasts are still very easily at the MTOCs, according to need.
ie
id

active and responsible for the coding and synthesis of

ev
br

certain vital proteins, but mitochondria and chloroplasts KEY WORDS

am

-R

can no longer live independently. Mitochondrial

ribosomes are just visible as tiny dark orange dots in the ADP (adenosine diphosphate): the molecule
-C

that is converted to ATP by addition of

s

mitochondrial matrix in Figure 1.28.

phosphate (a reaction known as phosphorylation)
es

during cell respiration; the enzyme responsible is

y

Pr

Microtubules and microtubule

op

ATP synthase; the reaction requires energy

ity
C

microtubules: tiny tubes made of a protein

organising centres (MTOCs) called tubulin and found in most eukaryotic cells;
rs
w

Microtubules are long, rigid, hollow tubes found in microtubules have a large variety of functions,
ie

ve

the cytoplasm. They are very small, about 25 nm in including cell support and determining cell
y
ev

op
ni

diameter. Together with actin filaments and intermediate shape; the ‘spindle’ on which chromatids and
R

filaments (not discussed in this book), they make up the chromosomes separate during nuclear division is
C

cytoskeleton, an essential structural component of cells made of microtubules

e

which helps to determine cell shape.

g

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a dimer

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b

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am 5 nm

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25 nm
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dimers can reversibly appearance in
y

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attach to a microtubule
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cross section

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C

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y
ev

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The dimers have a
The dimers form 13 protofilaments
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helical arrangement.

w
around a hollow core.

ie
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Figure 1.29: a The structure of a microtubule and b the arrangement of microtubules in two cells. The microtubules are

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coloured yellow.
am

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-C

Centrioles and centrosomes They lie close together and at right angles to each other
s

in a region known as the centrosome. Centrioles and the

es

centrosome are absent from most plant cells.

y

Note: Centrosomes are extension content, and

Pr
op

are not part of the syllabus. A centriole is a hollow cylinder about 500 nm long, formed
ity
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from a ring of short microtubules. Each centriole contains

The extra resolution of the electron microscope reveals nine triplets of microtubules (Figures 1.30 and 1.31).
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that just outside the nucleus of animal cells there are

ie

Until recently, it was believed that centrioles acted as

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really two centrioles and not one as it appears under

y
MTOCs for the assembly of the microtubules that make
ev

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ni

the light microscope (compare Figures 1.4 and 1.19). up the spindle during nuclear division (Chapter 5). It is
R

now known that this is done by the centrosome, but does

C

not involve the centrioles. However, centrioles are needed

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triplet of microtubules (one

w

complete microtubule and for the production of cilia. Centrioles are found at the
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two partial microtubules) bases of cilia and flagella, where they are known as basal
ev
br

bodies. The centrioles act as MTOCs. The microtubules

am

that extend from the basal bodies into the cilia and
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500 nm flagella are essential for the beating movements of these

-C

organelles.
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KEY WORDS
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centriole: one of two small, cylindrical structures,

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made from microtubules, found just outside the

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nucleus in animal cells, in a region known as the

ie

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200 nm centrosome; they are also found at the bases of

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ev

cilia and flagella

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Figure 1.30: The structure of a centriole. It consists of nine

R

centrosome: the main microtubule organising

C

groups of microtubules. Each group is made up of three

centre (MTOC) in animal cells
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microtubules, a triplet.
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Cilia and flagella

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Cilia (singular: cilium) and flagella (singular: flagellum)

ev
br
am have identical structures. They are whip-like, beating

-R
extensions of many eukaryotic cells. Each is surrounded
by an extension of the cell surface membrane. They
-C

were given different names before their structures were

s
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discovered: flagella are long and found usually one or
two per cell, whereas cilia are short and often numerous.
y

Pr
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Structure

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Cilia and flagella are extremely complicated structures,

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composed of over 600 different polypeptides. This

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Figure 1.31: Centrioles in transverse and longitudinal

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complexity results in very fine control of how they beat.
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section (TS and LS) (×86 000). The one on the left is seen in

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TS and clearly shows the nine triplets of microtubules which The structure of a cilium is shown in Figure 1.32.
R

C
make up the structure. Cilia have two central microtubules and a ring of nine
ge

microtubule doublets (MTDs) around the outside.

w
This is referred to as a ‘9 + 2’ structure. Each MTD

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id

KEY WORDS contains an A and a B microtubule (Figure 1.32a).

ev
br

The wall of the A microtubule is a complete ring of

cilia (singular: cilium): whip-like structures
am

-R13 protofilaments and the B microtubule attached

projecting from the surface of many animal cells is an incomplete ring with only 10 protofilaments
and the cells of many unicellular organisms; they
-C

(see Figure 1.32a). Figure 1.32a shows that each A

s

beat, causing locomotion or the movement of

es

microtubule has inner and outer arms. These are

fluid across the cell surface
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made of the protein dynein. They connect with the B

Pr
op

flagella (singular: flagellum): whip-like structures microtubules of neighbouring MTDs during beating. If
you imagine the microtubule in three dimensions, there
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projecting from the surface of some animal cells

C

and the cells of many unicellular organisms; they are two rows of several hundred dynein arms along the
rs
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beat, causing locomotion or the movement of outside of each A microtubule. The whole cylindrical
ie

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fluid across the cell surface; they are identical in structure inside the cell surface membrane is called the
y
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structure to cilia, but longer axoneme.

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C
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b
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Note: the structure of flagella is extension

content, and not part of the syllabus. cell surface membrane
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a
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9+2
cell surface membrane cilium
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outer arm
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inner arm
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2 singlet microtubules
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B B microtubule doublet
A
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A microtubule microtubule basal body 9 triplets

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Figure 1.32: The structure of a cilium. a A cilium seen in TS. Note the ‘9 + 2’ arrangement of microtubules.
e

b A cilium. TSs of the cilium (9 + 2) and basal body (9 triplets) are also shown.
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At the base of each cilium and flagellum is a structure
Question

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called the basal body which is identical in structure to

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the centriole. We now know that centrioles replicate 9 In vertebrates, beating cilia are also found on the

ev
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themselves to produce these basal bodies, and that cilia epithelial cells of the oviduct (the tube connecting
am the ovary to the uterus). Suggest what function cilia

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and flagella grow from basal bodies. Figure 1.33 is a
scanning electron micrograph of cilia in the respiratory have in the oviduct.
-C

tract.

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Chloroplasts
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Pr
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The structure of the chloroplast as seen with the electron

microscope is shown in Figures 1.20, 1.21 and 1.34.

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You can also see a higher-resolution micrograph in

rs
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Figure 13.4. Chloroplasts tend to have an elongated

ie

ve
shape and a diameter of about 3–10 μm (compare 1 μm

y
ev

diameter for mitochondria). Like mitochondria, they

op
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are surrounded by two membranes, which form the

R

C
chloroplast envelope.
ge

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The main function of chloroplasts is to carry out

ie
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photosynthesis. During the first stage of photosynthesis

ev
br

(the light-dependent stage), light energy is absorbed by

photosynthetic pigments, particularly chlorophyll. The
am

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pigments are found on the membranes of the chloroplast.
-C

The membrane system consists of fluid-filled sacs

s
es

Figure 1.33: Scanning electron micrograph of cilia in the called thylakoids, which spread out like sheets in three
dimensions. In places, the thylakoids form flat, disc-
y

respiratory tract
Pr
op

like structures that stack up like piles of coins, forming

structures called grana (from their appearance in the
ity
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Beating mechanism light microscope; ‘grana’ means grains).

rs
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The beating motion of cilia and flagella is caused by the

ie

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dynein (protein) arms making contact with, and moving KEY WORD
y
ev

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along, neighbouring microtubules. This produces the

thylakoid: a flattened, membrane-bound, fluid-
R

force needed for cilia to beat. As neighbouring MTDs

C

filled sac which is the site of the light-dependent

slide past each other, the sliding motion is converted
ge

reactions of photosynthesis in a chloroplast

w

into bending by other parts of the cilium.

ie
id

ev
br

Functions The second stage of photosynthesis (the light-

am

-R

If the cell is attached to something so that it cannot independent stage) uses the energy and reducing power
move, fluid will move past the cell. If the cell is not generated during the first stage to convert carbon dioxide
-C

attached, the cell will swim through the fluid. Single- into sugars. This takes place in the stroma. The sugars
s
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celled organisms can therefore use the action of cilia and made may be stored in the form of starch grains in the
y

flagella for locomotion. You will easily be able to find stroma (Figures 1.20 and 13.3 and 13.4).
Pr
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videos of such motion on the internet. In vertebrates, Lipid droplets are also seen in the stroma. They appear
beating cilia are found on some epithelial cells, such as
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as black spheres in electron micrographs (Figure 1.34).

those lining the airways (Chapter 9). Here more than They are reserves of lipid for making membranes or are
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10 million cilia may be found per mm2. They maintain formed from the breakdown of internal membranes as
ie

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a flow of mucus which removes debris such as dust and the chloroplast ages.
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bacteria from the respiratory tract.

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Like mitochondria, chloroplasts have their own protein

R

synthesising machinery, including 70S ribosomes and

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circular DNA. In electron micrographs, the ribosomes Some cell walls become even stronger and more rigid

w
can just be seen as small black dots in the stroma by the addition of lignin. Xylem vessel elements and

ie
id
(Figure 13.4). sclerenchyma are examples (Chapter 7). Lignin adds

ev
br
As with mitochondria, it has been shown that
am compressional strength to tensile strength (it prevents

-R
chloroplasts originated as endosymbiotic bacteria, buckling). It is what gives wood (secondary xylem) its
in this case photosynthetic blue-green bacteria. The strength and is needed for support in shrubs and trees.
-C

s
endosymbiont theory is discussed in more detail in the

es
earlier section on mitochondria. Functions
y

Pr
Some of the main functions of cell walls are summarised
op

below.
Cell walls

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• Mechanical strength and support for individual

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Structure cells and the plant as a whole. Lignification is one

ie

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means of support. Turgid tissues are another means
The first walls formed by plant cells are known as

y
ev

of support that is dependent on strong cell walls.

op
ni
primary walls. They are relatively rigid. The primary wall
R

consists of parallel fibres of the polysaccharide cellulose • Cell walls prevent cells from bursting by osmosis

C
running through a matrix of other polysaccharides if cells are surrounded by a solution with a higher
ge

w
such as pectins and hemicelluloses. Cellulose fibres are water potential (Chapter 2).

ie
id

inelastic and have high tensile strength, meaning they

• Different orientations of the layers of cellulose

ev
br

are difficult to break by pulling on each end. This makes

fibres help determine the shapes of cells as they
it difficult to stretch the wall, for example when water
am

-R grow.
enters the cell by osmosis. The structure of cellulose is
described in Chapter 2. • The system of interconnected cell walls in a plant
-C

is called the apoplast. It is a major transport route

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In most cells extra layers of cellulose are added to the for water, inorganic ions and other materials
y

first layer of the primary wall, forming a secondary

Pr

(Chapter 7).
op

wall. In a given layer the cellulose fibres are parallel, but

the fibres of different layers run in different directions • Living connections through neighbouring cell walls,
ity
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forming a cross-ply structure which is stronger as a the plasmodesmata, help form another transport
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result (see Figure 2.10). pathway through the plant known as the symplast
ie

(Chapter 7).
ve

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• The cell walls of the root endodermis are

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impregnated with suberin, a waterproof substance

R

lipid
C

droplet that forms a barrier to the movement of water, thus

ge

helping in the control of water and mineral ion

w

cell wall
uptake by the plant (Chapter 7).
ie
id

granum
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X • Epidermal cells often have a waterproof layer of

am

waxy cutin, the cuticle, on their outer walls. This

-R

helps reduce water loss by evaporation.

-C

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Vacuoles
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thylakoid As we have seen, animal cell vacuoles are relatively small

ity
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and include phagocytic vacuoles, food vacuoles and

autophagic vacuoles.
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Figure 1.34: Two chloroplasts (×16 000). Thylakoids (yellow)

ie

run through the stroma (dark green) and are stacked in

ve

Unlike animal cells, plant cells typically have a large

y

places to form grana. Black circles among the thylakoids are central vacuole (Figure 1.20). Some examples of the
ev

op
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lipid droplets. See also Figures 13.3 and 13.4. Chloroplast X functions of the large central vacuole of plants are listed
R

is referred to in Question 3b. below. It is useful to try to remember one or two of these
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examples.
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Support • Certain alkaloids and tannins deter herbivores from

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eating the plant.

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The solution in the vacuole is relatively concentrated.

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Water therefore enters the vacuole by osmosis, inflating •

br
Latex, a milky fluid, can accumulate in vacuoles,
the vacuole and causing a build-up of pressure. A fully
am for example in rubber trees. The latex of the opium

-R
inflated cell is described as turgid. Turgid tissues help poppy contains alkaloids such as morphine from
to support the stems of plants that lack wood (wilting which opium and heroin are obtained.
-C

s
demonstrates the importance of this).

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Food reserves
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Lysosomal activity
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Food reserves, such as sucrose in sugar beet, or mineral

Plant vacuoles may contain hydrolases and act as salts, may be stored in the vacuole. Protein-storing

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lysosomes. vacuoles are common in seeds.

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Secondary metabolites Waste products

y
ev

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Plants contain a wide range of chemicals known as Waste products, such as crystals of calcium oxalate, may
R

secondary metabolites which, although not essential be stored in vacuoles.

C
for growth and development, contribute to survival
ge

w
in various ways. These are often stored in vacuoles. Growth in size

ie
id

Examples of their functions are:

Osmotic uptake of water into the vacuole is responsible

ev
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• Anthocyanins are pigments that are responsible for for most of the increase in volume of plant cells during
am

most of the red, purple, pink and blue colours of

-R
growth. The vacuole occupies up to a third of the total
flowers and fruits. They attract pollinators and seed cell volume.
-C

dispersers.
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PRACTICAL ACTIVITY 1.3

op

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Work in groups of ten. Each group should make one copy of the following table on stiff card.
rs
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START Photosynthesis occurs in this organelle

ie

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Chloroplast Chromosomes are found in this structure in eukaryotic cells

op
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Nucleus These are found on rough endoplasmic reticulum (RER)

R

Ribosomes This structure contains cellulose as a strengthening material

ge

Cell wall Makes ribosomes

ie
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Nucleolus Site of ATP synthesis in aerobic respiration

br
am

Mitochondrion Makes lysosomes

-R

Golgi apparatus Has a ‘9 + 2’ arrangement of microtubules

-C

Cilium Mainly contains digestive enzymes

es

Lysosome END
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Cut up the card so that each piece of card has one term and one description (one row of the table). There are
ity
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therefore ten cards.

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Shuffle the cards and take one each. The student with the START card reads out the description and the
ie

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student who has the correct matching term reads out THE correct term from their card. They then read out the
ev

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description on their card. This continues until it reaches the END card. Your teacher will help if you get stuck.
R

The cards can be reshuffled and the activity repeated to see if you can do it faster the second time.
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1.7 Bacteria Structure of bacteria

w
ie
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Figure 1.35 shows the structure of a typical bacterium

ev
You will recall that there are two fundamental types

br
(plural: bacteria). The left side of the diagram shows the
of cell: prokaryotes and eukaryotes. The plant and
am

-R
structures that are always present. The right side of the
animal cells you have studied so far are eukaryotic cells.
diagram shows the structures which are sometimes found
Bacteria are prokaryotes and their cells are much simpler
-C

in bacteria.

s
than those of eukaryotes. Prokaryotic cells are generally

es
about 1000 times smaller in volume and lack a nucleus
y

KEY WORD

Pr
that is surrounded by a double membrane. Prokaryotes
op

are thought to have been the first living organisms on

bacteria (singular: bacterium): a group of single-

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Earth. The earliest known fossil prokaryotes are about

celled prokaryotic microorganisms; they have a
3.5 billion years old (the Earth was formed about

rs
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number of characteristics, such as the ability to

4.5 billion years ago). Most biologists believe that
ie

ve
form spores, which distinguish them from the
eukaryotes evolved from prokaryotes about 2 billion

y
ev

other group of prokaryotes known as Archaea

op
ni
years ago. There are two groups of prokaryotes, known
R

as Bacteria and Archaea. (The classification of living

C
organisms is discussed in Chapter 18.) We consider only
ge

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Bacteria in this book.

ie
id

ev
br

structures always structures sometimes

present present
am

-R
-C

s
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flagellum
y

for locomotion;
Pr
op

very simple structure

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cell wall
containing
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murein, a capsule or slime layer

ie

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peptidoglycan additional protection

y
ev

op
ni

infolding of cell
R

surface membrane
C

cell surface
may form a
ge

membrane
w

photosynthetic
ie
id

membrane or carry
ev

out nitrogen fixation

br

cytoplasm
am

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circular DNA plasmid

-C

small circle of DNA;

es

several may
y

be present
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ribosomes
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pili
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for attachment to
ie

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other cells or surfaces;

y

involved in sexual
ev

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reproduction
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C
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Figure 1.35: Diagram of a bacterium. Cells are generally about 1–5 µm in diameter.
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Cell wall bacteria, for example, the infolded membrane contains

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photosynthetic pigments which allow photosynthesis

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id
Bacterial cell walls contain a strengthening material called
to take place. In some bacteria, nitrogen fixation takes

ev
peptidoglycan. The cell wall protects the bacterium and is

br
place on the infolded membrane. Nitrogen fixation is
essential for its survival. It prevents the cell from swelling
am

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the ability to convert nitrogen in the air to nitrogen-
up and bursting if water enters the cell by osmosis.
containing compounds, such as ammonia, inside the cell.
-C

All life depends on nitrogen fixation. Eukaryotes cannot

s
KEY WORD

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carry out nitrogen fixation.
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Pr
peptidoglycan: a polysaccharide combined with
op

amino acids; it is also known as murein; it makes Capsule

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the bacterial cell wall more rigid Some bacteria are surrounded by an extra layer outside

rs
the cell wall. This may take the form of a capsule or a
w

slime layer. A capsule is a definite structure, made mostly

ie

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Cell surface membrane

y
of polysaccharides. A slime layer is more diffuse and is
ev

op
ni

Like all cells, bacterial cells are surrounded by a cell easily washed off. Both help to protect the bacterium
R

surface membrane. from drying out and may have other protective functions.

C
For example, a capsule helps protect some bacteria from
ge

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Cytoplasm antibiotics. Some capsules prevent white blood cells

ie
id

known as phagocytes from engulfing disease-causing

The cytoplasm does not contain any double membrane-

ev
br

bacteria.
bound organelles (such as mitochondria).
am

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Plasmid
Circular DNA
-C

A plasmid is a small circle of DNA separate from

The DNA molecule in bacteria is circular. It is found in
es

the main DNA of the cell. It contains only a few

a region called the nucleoid, which also contains proteins
y

genes. Many plasmids may be present in a given cell.

Pr
op

and small amounts of RNA. It is not surrounded by

The genes have various useful functions. Commonly,
a double membrane, unlike the nucleus of eukaryotes.
ity

plasmids contain genes that give resistance to particular

C

There may be more than one copy of the DNA molecule

antibiotics, such as penicillin. Plasmids can copy
rs
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in a given cell.
themselves independently of the chromosomal DNA
ie

ve

and can spread rapidly from one bacterium to another.

y
ev

Ribosomes Plasmid DNA is not associated with protein and is

op
ni

referred to as ‘naked’ DNA.

R

Bacterial ribosomes are 70S ribosomes, slightly smaller

C

than the 80S ribosomes of eukaryotes.

ge

KEY WORD
ie
id

Flagellum plasmid: a small circular piece of DNA in a

ev
br

Some bacteria are able to swim because they have one bacterium (not its main chromosome); plasmids
am

-R

or more flagella. Bacterial flagella have a much simpler often contain genes that provide resistance to
structure than eukaryotic flagella. The bacterial flagellum antibiotics
-C

is a simple hollow cylinder made of identical protein

s
es

molecules. It is a rigid structure, so it does not bend, unlike

Pili (singular: pilus)
y

the flagella in eukaryotes. It is wave-shaped and works by

Pr
op

rotating at its base like a propeller to push the bacterium Pili are fine protein rods. They vary in length and
through its liquid environment. As a result, the bacterium
ity
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stiffness. One to several hundred may be present on the

moves forward with a corkscrew-shaped motion. outside of the cell. They are used for attachment and
rs
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interactions with other cells or surfaces. They allow

ie

ve

Infolding of cell surface membrane the transfer of genes, including plasmids, from one
y
ev

op
ni

In some bacteria, the cell surface membrane folds bacterium to another during conjugation.
R

into the cell forming an extra surface on which certain

C

biochemical reactions can take place. In blue–green

e

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1.8 Comparing prokaryotic cells with eukaryotic cells

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ev
Table 1.3 compares prokaryotic cells with eukaryotic cells.

br
am

-R
Prokaryotes Eukaryotes
-C

Prokaryotes are thought to have evolved Eukaryotes are thought to have evolved about 1.5 billion

s
es
about 3.5 billion years ago. years ago.
y

Pr
Their typical diameter is 1–5 μm. Cells are up to 40 μm diameter and up to 1000 times the volume
op

of prokaryotic cells.

ity
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DNA is circular and free in the cytoplasm; it DNA is not circular and is contained in a nucleus. The nucleus is

rs
w

is not surrounded by a double membrane. surrounded by a double membrane (the nuclear envelope).
ie

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70S ribosomes are present (smaller than 80S ribosomes are present (larger than those of prokaryotes).

y
ev

op
ni

those of eukaryotes).
R

C
Very few types of cell organelle are Many types of cell organelle are present.
ge

present. No separate membrane-bound

w
organelles are present. • Some organelles are surrounded by a single membrane

ie
id

(e.g. lysosomes, Golgi apparatus, vacuoles, ER).

ev
br

• Some are surrounded by an envelope of two membranes

(e.g. nucleus, mitochondrion, chloroplast).
am

-R
• Some have no membrane (e.g. ribosomes, centrioles,
microtubules).
-C

s
es

The cell wall contains peptidoglycan (a A cell wall is sometimes present (e.g. in plants and fungi); it
y

polysaccharide combined with amino contains cellulose or lignin in plants, and chitin (a nitrogen-
Pr
op

acids). containing polysaccharide similar to cellulose) in fungi.

ity
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Flagella are simple and lack microtubules; Flagella (and cilia) are complex with a ‘9 + 2’
rs

they project outside the cell surface arrangement of microtubules; they are surrounded by the cell
w

membrane so they are extracellular surface membrane so they are intracellular (inside the cell).
ie

ve

y
(outside the cell).
ev

op
ni

Cell division occurs by binary fission (the Cell division takes place by mitosis or meiosis and involves a
R

cell splits into two); it does not involve a spindle (see Chapter 6).
ge

spindle (see Chapter 6).

w
ie
id

Some carry out nitrogen fixation. None carries out nitrogen fixation.
ev
br
am

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Table 1.3: Comparing prokaryotic cells and eukaryotic cells.

-C

Question tiny ‘particles’ which are much smaller than bacteria and
es

are on the boundary between what we think of as living

y

10 List the structural features that prokaryotic and and non-living. Unlike prokaryotes and eukaryotes,
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eukaryotic cells have in common. Briefly explain why viruses do not have a cell structure. In other words, they
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each of the structures you have listed is essential.

KEY WORD
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1.9 Viruses virus: a very small (20–300 nm) infectious particle

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which can replicate only inside living cells; it

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In 1852, a Russian scientist discovered that certain consists of a molecule of DNA or RNA (the
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diseases could be transmitted by agents that, unlike genome) surrounded by a protein coat; an outer
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bacteria, could pass through very fine filters. This was lipid envelope may also be present
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the first evidence for the existence of viruses. Viruses are

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1 Cell structure

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are not surrounded by a partially permeable membrane

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containing cytoplasm with ribosomes. They are much KEY WORD

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simpler in structure. They consist only of the following: phospholipid: a lipid to which phosphate is

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• a self-replicating molecule of DNA or RNA (the
am added; the molecule is made up of a glycerol

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genome or complete genetic instructions) molecule, two fatty acids and a phosphate
group; a double layer (a bilayer) of phospholipids
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• a protective coat of protein molecules called a capsid

s
forms the basic structure of all cell membranes

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• (some viruses only) a membrane-like outer layer,
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called the envelope, that is made of phospholipids.

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(The structure of phospholipids is described in Viruses range in size from about 20 nm to 300 nm (about
50 times smaller on average than bacteria).

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Chapter 2.) Proteins may project from the envelope.
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Figure 1.36 shows the structure of a virus with an All viruses are parasitic because they can only reproduce

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envelope. Viruses typically have a very symmetrical shape. by infecting and taking over living cells. The virus DNA or
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The protein coat (or capsid) is made up of separate RNA takes over the protein synthesising machinery of the

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protein molecules, each of which is called a capsomere. host cell, which then helps to make new virus particles.
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a b c Zika virus
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envelope protein
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envelope
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capsid
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DNA or RNA genome

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Figure 1.36: a The structure of a virus with an envelope; b model of a Zika virus. The virus is an RNA virus. Its capsid has
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an outer envelope; c electron micrograph of a cell infected by Zika virus. The virus particles are the darkly stained roughly
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spherical structures. Each virus particle is about 40 nm in diameter.

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REFLECTION
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Think about everything you know about cells. What being able to adapt the way you work? If not, what
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answers would you give to the following questions? particular concerns do you have?
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• What is a cell? You have studied cells in Chapter 1 and learnt a lot
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• Why are all living things made of cells? about their structure and function. The Reflection
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activity gives you a chance to use this information to

Look back at the differences between eukaryotic think again about cells from a slightly different point
and prokaryotic cells.
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of view.
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• Write down a list of criteria to compare the How did the Reflection activity improve your
success of prokaryotic and eukaryotic cells.
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understanding of what you have studied in Chapter 1?

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• Suggest why trying to compare the success

Final reflection
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of prokaryotic and eukaryotic cells may be a

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meaningless exercise. (Tip: think about the Discuss with a friend which, if any, parts of
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meaning of the word ‘success’.) Chapter 1 you need to:

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• read through again to make sure you really

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Personal reflection questions

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understand
Changing from studying at GCSE to studying at
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AS Level is a big jump. Has anything surprised • seek more guidance on, even after going over
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you about the change? Are you confident about it again.

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CAMBRIDGE INTERNATIONAL AS & A LEVEL BIOLOGY: COURSEBOOK

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SUMMARY

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The basic unit of life is the cell. The simplest cells are prokaryotic cells, which are thought to have evolved
before, and given rise to, the much more complex and much larger eukaryotic cells.
am

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Cells can be seen clearly only with the aid of microscopes. The light microscope uses light as a source of
-C

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radiation, whereas the electron microscope uses electrons. The electron microscope has greater resolution

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(allows more detail to be seen) than the light microscope because electrons have a shorter wavelength than light.
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With a light microscope, cells may be measured using an eyepiece graticule and a stage micrometer. Using the
I
formula A =

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the actual size of an object (A) or its magnification (M) can be found if its observed (image)
M

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size (I) is measured and A or M, as appropriate, is known.

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All cells are surrounded by a partially permeable cell surface membrane that controls exchange between the cell

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and its environment. All cells contain genetic material in the form of DNA, and ribosomes for protein synthesis.
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All eukaryotic cells possess a nucleus containing DNA. The DNA is linear (not circular) and bound to proteins
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and RNA to form chromatin.

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The cytoplasm of eukaryotic cells contains many organelles, some of which are surrounded by one or two

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membranes. Organelles of eukaryotic cells include endoplasmic reticulum (ER), 80S ribosomes, Golgi
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apparatus, lysosomes and mitochondria. Animal cells also contain a centrosome and centrioles and may
am

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contain cilia. Plant cells have a cell wall containing cellulose. They may contain chloroplasts and often have a
large central vacuole.
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Prokaryotic cells lack a true nucleus and have smaller (70S) ribosomes than eukaryotic cells. They also lack
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membrane-bound organelles. Their DNA is circular and lies free in the cytoplasm.
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Viruses do not have a cellular structure. They are extremely small and simple. They consist of a molecule of DNA or
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RNA, a protein coat and sometimes an outer envelope.

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EXAM-STYLE QUESTIONS
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1 Which one of the following cell structures can be seen with a light microscope?
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A mitochondrion C rough ER
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B ribosome D smooth ER [1]

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2 What property of electrons allows high resolution to be achieved

am

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by electron microscopes?
a Electrons are negatively charged.
-C

b Electrons can be focused using electromagnets.

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c Electrons have a very short wavelength.

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d Electrons travel at the speed of light. [1]

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3 Which one of the following structures is found in animal cells but

not in plant cells?
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A cell surface membrane

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B centriole
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C chloroplast
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D Golgi apparatus [1]

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Chapter 2
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Biological rs
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molecules
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LEARNING INTENTIONS
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In this chapter you will learn how to:

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• describe how large biological molecules are made from smaller molecules
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• describe the structure of carbohydrates, lipids and proteins and how their structure relates to their
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functions
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• describe and carry out biochemical tests to identify carbohydrates, lipids and proteins
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• explain some key properties of water that make life possible.

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CAMBRIDGE INTERNATIONAL AS & A LEVEL BIOLOGY: COURSEBOOK

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BEFORE YOU START

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It is useful to remind yourself of how atoms join nitrogen. Join the balls or jelly beans with short
together to make molecules. The best way to do
am sticks such as toothpicks, matchsticks or straws. The

-R
this is to draw or make models of some simple sticks represent covalent bonds.
molecules. You want to show how the carbon,
-C

s
hydrogen, oxygen and nitrogen atoms are joined Try making models of or drawing these molecules:

es
together with covalent bonds. Carbon has four • methane, CH4
y

Pr
bonds, nitrogen three, oxygen two and hydrogen
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one. The bonds should be arranged with the • water, H2O

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correct orientation (see Figures 2.11, 2.16, 2.23

• ethanol, C2H5OH
and 2.27 to help you).
rs
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• a hydrocarbon, e.g. C3H8

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If you can, use model kits. Otherwise, coloured

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balls of modelling clay (or coloured jelly beans) can

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• ammonia, NH3
be used to represent atoms. Use black for carbon,
R

C
white for hydrogen, red for oxygen and blue for • ethanoic acid, CH3COOH.
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THE PROTEIN-FOLDING PROBLEM – FROM DEEP BLUE TO ALPHAZERO AND BEYOND

am

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In 1962, two Cambridge scientists, John For example, Demis Hassabis has suggested that,
Kendrew and Max Perutz, received the Nobel in the future, AlphaZero and computers like it
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Prize for Chemistry for their work on the three- may be able to design more effective drugs and
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dimensional structure of the proteins myoglobin medicines. One of the key problems in biology
y

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and haemoglobin. The work was a vital step in is the so-called ‘protein-folding problem’. This is
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understanding how proteins function. Thirty-five the problem of trying to discover the rules of how
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years later, in 1997, a world chess champion, Garry proteins fold into the precise three-dimensional
Kasparov, was beaten at chess for the first time by shapes essential for their functions. Ideally, knowing
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the computer Deep Blue. So what is the connection the primary structure of a protein and its chemical
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between these two events? environment (e.g. pH and temperature) would

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enable scientists to predict how the protein will fold

The answer lies in the applications of artificial
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up. The work has vital applications. For example,

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intelligence (AI). The IBM computer Deep Blue was

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an important milestone on the road to developing

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AI. One of the most exciting recent computers to

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be developed is AlphaZero, the creation of another

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British scientist, Demis Hassabis. AlphaZero has

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taught itself to be the best chess player ever. It

took only four hours starting from scratch, using
-C

the technique known as ‘reinforcement learning’ –

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learning by trial and error by playing millions of

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games against itself.

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How can a computer like this be of use to humans?

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There are many problems in the world, such as

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climate change, which are too complex for the

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human brain to analyse fully. AI may help. Some of

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the problems that AI is beginning to tackle relate to

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biological molecules.
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Figure 2.1: The protein-folding problem.

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2 Biological molecules

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CONTINUED

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many diseases and disorders including Alzheimer’s, to the goal of predicting how proteins will fold,

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Parkinson’s and cystic fibrosis are caused by faulty
am but it seems only AI can provide all the answers

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protein folding. In December 2018, the computer (Figure 2.1).
AlphaFold won an international contest to predict
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Questions for discussion

s
protein structure more accurately than previous

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attempts. Can you think of any potential problems with AI?
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Do you think the benefits outweigh these problems,

Pr
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Around 60 years after the pioneering work of or not?

Kendrew and Perutz, scientists are getting closer

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2.1 Biochemistry

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organic amino fatty acids
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monosaccharides

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bases acids and glycerol

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Biochemistry looks at the chemical reactions of

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biological molecules. The sum total of all the biochemical
ge

w
reactions in the body is known as metabolism. You nucleotides

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may think biochemistry is a complicated subject, but

ev
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it has an underlying simplicity. For example, only

nucleic
am

20 common amino acids are used to make proteins,

-R polysaccharides proteins lipids
whereas theoretically there could be millions. Having a acids
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limited variety of molecules makes it easier to control

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metabolism.
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simple biological complex biological

molecules molecules
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Another feature of biochemistry is the close link

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between the structures of molecules and their functions.

Figure 2.2: The building blocks of life are simple biological
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This will become clear in this chapter and in Chapter 3.

C

molecules which join together to form larger more complex

rs
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molecules.
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2.2 The building blocks

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of life 2.3 Monomers, polymers

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C
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The four most common elements in living organisms

and macromolecules
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are, in order of abundance, hydrogen, carbon, oxygen

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and nitrogen. They account for more than 99% of the A macromolecule is a giant molecule. There are three
ev
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atoms found in all living things. Carbon is particularly types of macromolecule in living organisms:
am

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important because carbon atoms can join together

• polysaccharides
to form long chains or ring structures. They can be
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• proteins (polypeptides)
s

thought of as the basic skeletons of organic molecules

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(molecules that contain carbon). Other atoms, with • nucleic acids (polynucleotides).
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different functions, are attached to the carbon skeletons.

Pr
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It is believed that, before life evolved, there was a

KEY WORD
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period of chemical evolution in which simple carbon-

based biological molecules evolved from even simpler
rs
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macromolecule: a large molecule such as a

molecules. The simple biological molecules are relatively
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polysaccharide, protein or nucleic acid

limited in variety. They act as the building blocks for
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ev

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larger, complex biological molecules (Figure 2.2).

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CAMBRIDGE INTERNATIONAL AS & A LEVEL BIOLOGY: COURSEBOOK

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The words polysaccharides, polypeptides and acids and nucleotides respectively (Figure 2.2.) Figure 2.2

w
polynucleotides all contain the term poly. ‘Poly’ means also shows the role of organic bases (not monomers) in

ie
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many. Macromolecules are described as polymers nucleotides and the role of fatty acids and glycerol in the

ev
br
because they are made up of many repeating subunits
am formation of lipids (not polymers).

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that are similar or identical to each other. The subunits
Cellulose and rubber are examples of naturally
are called monomers (‘mono’ means one). Monomers
occurring polymers. There are many examples of
-C

are joined together by covalent bonds. These are bonds

s
industrially produced polymers, such as polyester,

es
in which the atoms are joined by sharing electrons.
polythene, PVC (polyvinyl chloride) and nylon. All these
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Covalent bonds are relatively strong bonds. Examples

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are made up of carbon-based monomers and contain
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you will learn about in this chapter are the glycosidic

thousands of carbon atoms joined end to end.
bond, the ester bond and the peptide bond.

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Let’s now look at some of the small biological molecules

Making biological polymers from monomers is

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(monosaccharides, fatty acids and amino acids) and the

relatively simple because the same reaction is repeated
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larger molecules (carbohydrates, lipids and proteins)
many times. The reaction involves joining together

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ev

made from them. Organic bases, nucleotides and nucleic

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two monomers by the removal of a water molecule.
acids are discussed in Chapter 6.
R

This type of reaction is called a condensation reaction.

C
The opposite reaction (adding water) can be used to
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break down the polymer again. Adding water to split
2.4 Carbohydrates

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a molecule is called hydrolysis. You will meet many

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examples of condensation and hydrolysis in this chapter. All carbohydrates contain the elements carbon,
am

The monomers from which polysaccharides, proteins

-R hydrogen and oxygen. The ‘hydrate’ part of the name
and nucleic acids are made are monosaccharides, amino refers to water; the hydrogen and oxygen atoms are
-C

present in the ratio of 2 : 1 as in water. The general

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KEY WORDS formula for a carbohydrate can be written as Cx(H2O)y.

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Pr

Carbohydrates are divided into three main groups:

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polymer: a giant molecule made from many similar

monosaccharides, disaccharides and polysaccharides.
repeating subunits joined together in a chain; the
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The word ‘saccharide’ means a sugar or sweet substance.

subunits are much smaller and simpler molecules
rs
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known as monomers; examples of biological

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polymers are polysaccharides, proteins and

Monosaccharides
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nucleic acids
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Monosaccharides are sugars. Sugars dissolve easily in

R

monomer: a relatively simple molecule which is

C

water to form sweet-tasting solutions. Monosaccharides

used as a basic building block for the synthesis of
ge

consist of a single sugar molecule (‘mono’ means

w

a polymer; many monomers are joined together one, ‘saccharide’ means sugar). They have the general
ie
id

by covalent bonds to make the polymer, usually formula (CH2O)n. The main types of monosaccharides
ev
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by condensation reactions; common examples (when classified according to the number of carbon
of monomers are monosaccharides, amino acids
am

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atoms in each molecule) are trioses (3C), pentoses (5C)

and nucleotides and hexoses (6C). The names of all sugars end with -ose.
-C

Common hexoses are glucose, fructose and galactose.

s

condensation reaction: a chemical reaction

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involving the joining together of two molecules Two common pentoses are ribose and deoxyribose.
y

by removal of a water molecule

Pr
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hydrolysis: a chemical reaction in which a

Molecular and structural formulae
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chemical bond is broken by the addition of a The molecular formula for a hexose can be written
as C6H12O6. It means there are 6 carbon atoms, 12
rs
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water molecule; commonly used to break down

hydrogen atoms and 6 oxygen atoms in the molecule. It
ie

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complex molecules into simpler molecules

y

is useful to show the arrangements of the atoms using

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monosaccharide: a molecule consisting of a a diagram known as the structural formula. Figure 2.3
R

single sugar unit and with the general formula shows the structural formula of glucose, the most
C

(CH2O)n. common monosaccharide. Glucose is a hexose.

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H H (Figure 2.4). The ring therefore contains oxygen, and

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carbon atom number 6 is not part of the ring.

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C O C O

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You will see from Figure 2.4 that the hydroxyl group,
am –OH, on carbon atom 1 may be above or below the

-R
H C O H H C OH plane of the ring. The form of glucose where it is
below the ring is known as α-glucose (alpha-glucose)
-C

more

s
H O C H HO C H and the form where it is above the ring is β-glucose

es
commonly
shown as (beta-glucose). Two forms of the same chemical are
y

H C O H H C OH

Pr
known as isomers, and the extra variety provided by the
op

existence of α- and β-isomers has important biological

ity
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H C O H H C OH consequences, as you will see in the structures of starch,

glycogen and cellulose.

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H C O H CH2OH
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Question

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H
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C
1 The formula for a hexose is C6H12O6 or (CH2O)6.
Figure 2.3: Structural formula of glucose. –OH is known as
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What would be the formula of:

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a hydroxyl group. There are five in glucose.
a a triose?

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b a pentose?

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Ring structures Functions of monosaccharides in
living organisms
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One important aspect of the structure of pentoses

s

and hexoses is that the chain of carbon atoms is long Monosaccharides have two major functions. First,
es

enough to close up on itself to form a more stable ring they are commonly used as a source of energy in
y

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structure. When glucose forms such a ring, carbon atom respiration. This is due to the large number of carbon–
number 1 joins to the oxygen on carbon atom number 5 hydrogen bonds. These bonds can be broken to release
ity
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OH
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6
CH2OH
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5
C O O
H H
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4 H 1
H C C or, more
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OH H OH
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1 OH
simply OH OH
C O OH
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3 2
C C
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2
H C OH OH
H OH
am

α-glucose
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3
HO C H
OH
-C

4
H C OH
s

6
CH2OH
es

5
H C OH 5
C O O
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H OH OH
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6
CH2OH H
4 1
C C or, more
ity
C

OH H OH
simply
OH H OH
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glucose straight-chain form 3

C 2
C
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with C atoms numbered

H OH OH
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β-glucose
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Figure 2.4: Structural formulae for the straight-chain and ring forms of glucose. Chemists often leave out the C and H atoms
e

from the structural formula for simplicity.

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a lot of energy, which is transferred to help make

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ATP (adenosine triphosphate) from ADP (adenosine KEY WORD

ie
id
diphosphate) plus phosphate during the process of disaccharide: a sugar molecule consisting of

ev
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respiration. The most important monosaccharide in
am two monosaccharides joined together by a

-R
energy metabolism is glucose. glycosidic bond
Second, monosaccharides are important as building
-C

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blocks for larger molecules. For example, glucose is

es
bought in shops. Lactose is the sugar found in milk
used to make the polysaccharides starch, glycogen and
y

and is therefore an important constituent of the diet of

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cellulose. Ribose (a pentose) is one of the molecules
op

young mammals.
used to make RNA (ribonucleic acid) and ATP.

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Deoxyribose (also a pentose) is one of the molecules The process of joining two monosaccharides is an
used to make DNA (Chapter 6). example of a condensation reaction (Figure 2.5; see also

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Section 2.3, Monomers, polymers and macromolecules).

ie

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The reverse process (splitting a disaccharide into

y
Disaccharides and the
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two monomers) is also shown in Figure 2.5 and is an
R

glycosidic bond
U

example of a hydrolysis reaction. Notice that fructose

C
has a different ring structure from glucose.
ge

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Disaccharides, like monosaccharides, are sugars. They

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are formed by two monosaccharides joining together
id

For each condensation reaction, two hydroxyl (–OH)

(‘di’ means two). The three most common disaccharides

ev
groups line up alongside each other. One combines
br

are maltose (glucose + glucose), sucrose (glucose + with a hydrogen atom from the other to form a water
am

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fructose) and lactose (glucose + galactose). Sucrose is molecule. This allows an oxygen ‘bridge’ to form
the transport sugar in plants and the sugar commonly between the two molecules, holding them together
-C

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a monosaccharide monosaccharide disaccharide

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6 6 6 6
CH2OH CH2OH CH2OH CH2OH
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5 O 5 O 5 O 5 O
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–H2O (condensation)
4 1 4 1 4 1 4 1
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OH OH +H2O (hydrolysis) OH O OH
y
OH OH OH OH OH OH
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2 2 2 2
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3 3 3 3
R

OH H2O OH OH glycosidic bond OH

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α-glucose α-glucose maltose

ge

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b monosaccharide monosaccharide disaccharide

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6 6
CH2OH OH CH2OH OH
am

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5 O 1CH OH 3 4 5 O 1CH OH 3 4
2 2
–H2O (condensation)
-C

4 1 2 5 4 1 2 5
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OH 6 CH OH +H2O (hydrolysis) OH O 6 CH OH
OH 2 OH OH 2 OH 2 2
y

O O
Pr

3 3
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OH H2O OH glycosidic bond

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α-glucose β-fructose
C

sucrose
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Figure 2.5: Formation of a disaccharide from two monosaccharides by condensation. a Maltose is formed from two
ie

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α-glucose molecules. This can be repeated many times to form a polysaccharide. Note that in this example the glycosidic
ev

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bond is formed between carbon atoms 1 and 4 of neighbouring glucose molecules. b Sucrose is made from an α-glucose
R

and a β-fructose molecule.

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and forming a disaccharide. The bridge is called a The addition of water in hydrolysis takes place during

w
glycosidic bond. the digestion of disaccharides and polysaccharides,

ie
id
when they are broken down to monosaccharides.

ev
br
In theory, any two –OH groups can line up and, since
monosaccharides have many –OH groups, there are a
am

-R
large number of possible disaccharides. The shape of the KEY WORD
enzyme controlling the reaction determines which –OH
-C

glycosidic bond: a C–O–C link between two

s
groups come alongside each other. Only a few of the

es
sugar molecules, formed by a condensation
possible disaccharides are common in nature.
y

reaction; it is a covalent bond

Pr
op

ity
C

PRACTICAL ACTIVITY 2.1

rs
w
ie

ve
Testing for the presence of sugars As long as you use excess Benedict’s reagent

y
ev

op
ni
(more than enough to react with all of the sugar
1 Reducing sugars
R

present), the intensity of the red colour is related to

C
Reducing sugars are so called because they can the concentration of the reducing sugar. The test
ge

w
carry out a type of chemical reaction known as can therefore be used as a semi-quantitative test.

ie
id

reduction. In the process they are oxidised. The You can estimate the concentration of a reducing

ev
sugar solution using colour standards made by
br

reducing sugars include all monosaccharides

and some disaccharides. The only common non- comparing the colour against the colours obtained
am

-R
reducing sugar is sucrose. in tests done with reducing sugar solutions of known
concentration. You could also measure the time
-C

The ability of some sugars to carry out reduction taken for the first colour change.
es

is the basis of Benedict’s test for the presence of

y

sugar. The test uses Benedict’s reagent which is Alternatively, you can use a colorimeter to measure
Pr
op

copper(II) sulfate in an alkaline solution. It has a small differences in colour more precisely.
ity

distinctive blue colour. Reducing sugars reduce the

C

soluble blue copper sulfate to insoluble brick-red 2 Non-reducing sugars

rs
w

copper oxide, containing copper(I). The copper Some disaccharides, such as sucrose, are not
ie

ve

oxide is seen as a brick-red precipitate. reducing sugars, so you would get a negative result
y
ev

op
ni

from Benedict’s test. In such a case, you should then

reducing sugar + Cu2+ → oxidised sugar + Cu+
R

carry out the test for a non-reducing sugar.

U

blue red-brown
ge

In the non-reducing sugars test, the disaccharide

w

is first broken down into its two monosaccharide

ie

Procedure
id

constituents. The chemical reaction is hydrolysis and

ev
br

Add Benedict’s reagent to the solution you are can be brought about by adding hydrochloric acid.
am

testing and heat it in a water bath. If a reducing

-R

The constituent monosaccharides will be reducing

sugar is present, the solution will gradually turn sugars and their presence can be tested for using
-C

through green, yellow and orange to red-brown as Benedict’s test after the acid has been neutralised.
s

the insoluble copper(I) oxide forms a precipitate.

es

Procedure
y

Pr
op

KEY WORD
Carry out Benedict’s test on the solution. If you get a
ity
C

Benedict’s test: a test for the presence of negative result, start again with a fresh sample of the
reducing sugars; the unknown substance is solution. Heat the solution with hydrochloric acid. If
rs
w

heated with Benedict’s reagent, and a change a non-reducing sugar is present, it will break down to
ie

ve

monosaccharides. Benedict’s reagent needs alkaline

y

from a clear blue solution to the production of

ev

op
ni

a yellow, red or brown precipitate indicates the conditions to work, so you need to neutralise the
R

test solution now by adding an alkali such as sodium

U

presence of reducing sugars such as glucose

C
e

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ni
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C
ge

w
CONTINUED

ie
id
hydroxide. Add Benedict’s reagent and heat as before in the Benedict’s test. If there is still no colour change,

ev
br
and look for the colour change. If the solution now
am then there is no sugar of any kind present.

-R
goes red, a non-reducing sugar is present. If both a
reducing sugar and a non-reducing sugar are present, (See Practical Investigation 2.1 in the Practical
-C

Workbook for additional information.)

s
the precipitate will be heavier than the one obtained

es
y

Pr
op

Question they are linked between carbon atoms 1 and 4

ity
C

of successive glucose units.) The chains are curved

2 a Why do you need to use excess Benedict’s (Figure 2.6) and coil up into helical structures like

rs
w

reagent to find the concentration of a sugar springs, so the final molecule is compact.
ie

ve
solution?

y
ev

Amylopectin is also made of many 1,4 linked α-glucose

op
ni

b Outline how you could use the Benedict’s test molecules, but the chains are shorter than in amylose
R

to estimate the concentration of a solution of

C
and also contain 1,6 linkages. These start branches out
a reducing sugar.
ge

to the sides of the chain (Figure 2.7).

w
ie
id

Mixtures of amylose and amylopectin molecules build

Polysaccharides
ev
up into relatively large starch grains. Starch grains are
br

commonly found in chloroplasts and in storage organs,

am

Polysaccharides are polymers made by joining many

-R
such as potato tubers and the seeds of cereals and
monosaccharide molecules by condensation. Each legumes (Figure 2.8). Starch grains are easily seen with a
-C

successive monosaccharide is added by means of a

s
es

glycosidic bond, as in disaccharides. The final molecule may O 1 4 O

y

be several thousand monosaccharide units long, forming a

Pr
op

macromolecule. The most important polysaccharides are O

O O
starch, glycogen and cellulose, all of which are polymers of
ity
C

glucose. Polysaccharides are not sugars.

rs
w
ie

ve

Starch and glycogen

y
ev

op
ni

Since glucose is the main source of energy for cells, it

R

is important for living organisms to store glucose in an

ge

appropriate form. If glucose itself accumulated in cells,

w

it would dissolve and make the contents of the cell too

ie
id

concentrated. This would seriously affect the osmotic

ev
br

properties of the cell (Chapter 4, Section 4.5, Movement of

am

-R

substances across membranes). Glucose is also a reactive Figure 2.6: Arrangement of α-glucose units in amylose.
molecule and would interfere with normal cell chemistry. The 1,4 linkages cause the chain to turn and coil. The
-C

These problems are avoided when glucose is converted

s

glycosidic bonds are shown in red and the hydroxyl groups

es

by condensation reactions to a storage polysaccharide. are omitted.

y

The storage polysaccharide is a convenient, compact,

Pr
op

inert (unreactive) and insoluble molecule. The storage

polysaccharide in plants is starch; in animals, it is glycogen. KEY WORDS
ity
C

When needed, glucose is quickly made available again by

rs

polysaccharide: a polymer whose subunits are

w

enzyme-controlled hydrolysis reactions.

monosaccharides joined together by glycosidic
ie

ve

Starch is a mixture of two substances – amylose and

y

bonds
ev

op
ni

amylopectin. Amylose is made by condensations

glycogen: a polysaccharide made of many
R

between α-glucose molecules (Figure 2.5a). In this way,

C

glucose molecules linked together, that acts as a

a long, unbranching chain of several thousand 1,4
e

glucose store in liver and muscle cells

w

linked glucose molecules is built up. (‘1,4 linked’ means

g

ie
id

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2 Biological molecules

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U

C
ge
a glycosidic bond between b

w
C atoms 1 and 6 of neighbouring

ie
id
glucose units (1,6 link) 1,4 links

ev
br
am 1,6 link

-R
6
removal of
1,4 chain O 5 O water
-C

1 4 1
(condensation)

s
3 2

es
O O OH H 2O
y

Pr
op

6
CH2OH 1,4 links

ity
C

5 O
1,4 chain

rs
w

4 1
ie

ve 3 2
O O

y
ev

op
ni
R

Figure 2.7: Branching structure of amylopectin and glycogen. a Formation of a 1,6 link, making a branchpoint; b overall
U

C
structure of an amylopectin or glycogen molecule. Amylopectin and glycogen differ only in the amount of branching of
ge

w
their glucose chains; glycogen is more branched than amylopectin.

ie
id

ev
br

light microscope, especially if stained. Rubbing a freshly granules, which are visible in liver cells (see Figure 1.18)
am

cut potato tuber on a glass slide and staining with

-R
and muscle cells, where they form an energy reserve.
iodine–potassium iodide solution (Practical Activity 2.2)
-C

is a quick method of preparing a specimen for viewing.

s

Questions
es
y

Pr

3 What type of chemical reaction happens when

op

glucose is formed from starch or glycogen?

ity
C

4 List five ways in which the molecular structures

rs
w

of glycogen and amylopectin are similar.

ie

ve

y
ev

PRACTICAL ACTIVITY 2.2

op
ni
R

Testing for the presence of starch

ge

Starch molecules tend to curl up into long spirals.

ie
id

The hole that runs down the middle of this spiral

ev
br

is just the right size for iodine molecules to fit

into. To test for starch, you use ‘iodine solution’.
am

-R

(Iodine doesn’t dissolve in water; iodine solution

is actually iodine in potassium iodide solution.)
-C

The starch–iodine complex that forms has a strong

es

blue-black colour.
y

Pr

Figure 2.8: False-colour scanning electron micrograph of a

op

slice through a raw potato showing cells containing starch Procedure

ity
C

grains or starch-containing organelles (coloured red) (×260).

Iodine solution is orange-brown. Add a drop of
rs
w

iodine solution to the solid or liquid substance to

ie

ve

Starch is never found in animal cells. Glycogen is the be tested. A blue-black colour is quickly produced
y

storage carbohydrate in animals. It has molecules very like

ev

if starch is present.
op
ni

those of amylopectin because it is made of chains of 1,4

R

linked α-glucose with 1,6 linkages making branch points (See Practical Investigation 2.1 in the Practical
C

Workbook for additional information.)

e

(Figure 2.7b). Glycogen molecules clump together to form

w
g

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id

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br
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op
ni
U

C
ge
Cellulose also to oxygen atoms of –OH groups in neighbouring

w
molecules. These hydrogen bonds are individually weak,

ie
id
Cellulose is the most abundant organic molecule on the
but there are so many of them (due to the large number

ev
br
planet. This is due to its presence in plant cell walls and
of –OH groups) that collectively they provide enormous
its slow rate of breakdown in nature. It has a structural
am

-R
strength. Between 60 and 70 cellulose molecules become
role because it is a mechanically strong molecule, unlike
tightly cross-linked by hydrogen bonding to form
starch and glycogen. The only difference is that cellulose
-C

bundles called microfibrils. Microfibrils are in turn held

s
is a polymer of β-glucose, and starch and glycogen are

es
together by hydrogen bonding in bundles called fibres.
polymers of α-glucose.
y

Pr
A cell wall typically has several layers of fibres, running
op

KEY WORD in different directions to increase strength (Figure 2.10).

ity
C

Cellulose makes up about 20–40% of the average cell

cellulose: a polysaccharide made from beta- wall; other molecules help to cross-link the cellulose
rs
w

glucose subunits; used as a strengthening fibres, and some form a glue-like matrix around the
ie

ve
material in plant cell walls fibres, which further increases strength.

y
ev

op
ni

Cellulose fibres have a very high tensile strength, almost

R

C
equal to that of steel. This means that, if pulled at both
Remember that the –OH group on carbon atom 1
ge

ends, they are very difficult to stretch or break. The high

w
projects above the ring in the β-isomer of glucose tensile strength of the cellulose fibres makes it possible

ie
id

(Figure 2.4). In order to form a glycosidic bond with for a cell to withstand the large pressures that develop

ev
br

carbon atom 4, where the –OH group is below the ring, within it as a result of osmosis (Chapter 4, Section 4.5,
am

one glucose molecule must be upside down (rotated

-R
Movement of substances across membranes). Without
180°) relative to the other. Thus successive glucose units the wall, the cell would burst when in a dilute solution.
-C

are linked at 180° to each other (Figure 2.9). These pressures help provide support for the plant
s
es

This arrangement of β-glucose molecules results in a by making tissues rigid, and are responsible for cell
y

strong molecule because the hydrogen atoms of –OH expansion during growth. The arrangement of fibres
Pr
op

groups are weakly attracted to oxygen atoms in the same around the cell helps to determine the shape of the cell
as it grows.
ity

cellulose molecule (the oxygen of the glucose ring) and

C

Despite their strength, cellulose fibres are freely

rs
w

a
permeable, allowing water and solutes to reach or leave
ie

ve

OH groups lined up to the cell surface membrane.

y
ev

op
ni

form a glycosidic bond

6
R

β-glucose
C

O
5 3 2 rotated Question
ge

OH OH
w

180°
5 Make a table to show three ways in which the
ie
id

4 1 4 1
molecular structures of amylose and cellulose
ev
br

OH 3 2 5 OH differ.
am

O
-R

6
β-glucose (only the relevant
Dipoles and hydrogen bonds
-C

–OH groups are shown)

es

When atoms in molecules are held together by covalent

y

b
Pr

bonds, they share electrons with each other. Each shared

op

O O O O O O
pair of electrons forms one covalent bond. For example,
ity
C

O O O O O in a water molecule, two hydrogen atoms each share

a pair of electrons with an oxygen atom, forming a
rs
w

molecule with the formula H2O.

ie

ve

Figure 2.9: a Two β-glucose molecules lined up to form a

y
ev

1,4 link. Note that one glucose molecule must be rotated oxygen atom
op
ni

180° relative to the other. b Arrangement of β-glucose units

R

covalent bond
U

O
C

in cellulose: glycosidic bonds are shown in red and hydroxyl

H H
e

groups are omitted. hydrogen atom

w
g

ie
id

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br
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2 Biological molecules

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ni
U

C
ge

w
ie
id

ev
br
am

-R
-C

s
cell wall cellulose fibre microfibril

es
(50 nm diameter) (10 nm diameter)
y

made of many

Pr
op

microfibrils
glycosidic bond

ity
C

made of 60–70

rs
w

molecules
ie

ve

y
ev

op
ni
R

C
glucose ring structure – part hydrogen bond
ge

w
of one cellulose molecule

ie
id

ev
br

Figure 2.10: Structure of cellulose.

am

-R
However, the electrons are not shared absolutely equally. hydrogen bonds affect the properties of water in
-C

In water, the oxygen atom gets slightly more than its Section 2.7, Water.
s

fair share, and so has a small negative charge, written

es

Dipoles occur in many different molecules, particularly

δ− (delta minus). The hydrogen atoms get slightly less
y

where there is an –OH, –CO or –NH group. Hydrogen

Pr
op

than their fair share, and so have a small positive charge,

bonds can form between these groups, because the
written δ+ (delta plus).
ity
C

negatively charged part of one group is attracted to

This unequal distribution of charge is called a dipole: the positively charged part of another. These bonds
rs
w

δ− are very important in the structure and properties of

ie

ve

O carbohydrates and proteins.

y
ev

δ+ H H δ+
op
ni

Molecules that have groups with dipoles, such as sugars,

R

In water, the negatively charged oxygen of one molecule are said to be polar. Polar molecules are attracted to
C

is attracted to a positively charged hydrogen of another,

ge

water molecules because the water molecules also have

w

and this attraction is called a hydrogen bond. The dipoles. Such molecules are hydrophilic (water-loving),
ie
id

hydrogen bond is traditionally shown as a dotted or and tend to be soluble in water. Molecules which do
ev
br

dashed line in diagrams: not have dipoles are said to be non-polar. They are
am

δ− δ+ not attracted to water, and so, are hydrophobic (water-

-R

C O H N
hating). Such properties make possible the formation of
-C

cell membranes (Chapter 4).

s

It is much weaker than a covalent bond, but still

es

has a very significant effect. You will find out how

y

Pr
op

KEY WORD 2.5 Lipids

ity
C

Lipids are a very varied group of chemicals. They are

rs
w

hydrogen bond: a relatively weak bond formed all organic molecules which are insoluble in water.
ie

by the attraction between a group with a small

ve

Most lipids are formed by fatty acids combining with

y

positive charge on a hydrogen atom (Hδ+) and

ev

an alcohol. The most familiar lipids are fats and oils.

op
ni

another group carrying a small negative charge Fats are solid at room temperature and oils are liquid at
R

(δ−), e.g. between two –Oδ– Hδ+ groups

C

room temperature, but chemically they are very similar.

e

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ni
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C
ge
Fatty acids Alcohols and esters

w
ie
id
Fatty acids are a series of acids, some of which are found Alcohols are a series of organic molecules which

ev
br
in lipids. They contain the acidic group –COOH, known
am contain a hydroxyl group, –OH, attached to a carbon

-R
as a carboxyl group. The carboxyl group forms the ‘head’ atom. Glycerol is an alcohol with three hydroxyl groups
of the fatty acid molecule. The common fatty acids have (Figure 2.12).
-C

long hydrocarbon tails attached to the carboxyl group

s
The reaction between an acid and an alcohol produces a

es
(Figure 2.11). As the name suggests, the hydrocarbon
chemical known as an ester. The chemical link between
tail consists of a chain of carbon atoms combined with
y

Pr
the acid and the alcohol is called an ester bond or an
op

hydrogen. The chain is often 15 or 17 carbon atoms long.

ester linkage.

ity
C

The tails of some fatty acids have double bonds between

neighbouring carbon atoms, like this: –C C–. Such

rs
w

fatty acids are described as unsaturated because they do C COOH + HO C C COOC + H2O
ie

ve
not contain the maximum possible amount of hydrogen.

y
ev

op
ni
They form unsaturated lipids. Double bonds make fatty acid alcohol ester
R

acids and lipids melt more easily – for example, most oils

C
are unsaturated. If there is more than one double bond,
ge

KEY WORD

w
the fatty acid or lipid is described as polyunsaturated; if

ie
id

there is only one, it is monounsaturated. ester bond / ester linkage: a chemical bond,

ev
br

Animal lipids are often saturated (no double bonds) and represented as –COO– , formed when an acid
am

reacts with an alcohol

occur as fats, whereas plant lipids are often unsaturated
-R
and occur as oils, such as olive oil and sunflower oil.
-C

s
es
y

Pr
op

ity
C

rs
w
ie

OH O OH O
ve

acid head
y
C C
ev

op
ni

H C H H C H
C
R

H H H C H
U

hydrophobic
C

H C H H C H
hydrocarbon tail
ge

H C H H C H
w

H C H H C H
ie
id

H C H H C H
ev
br

H C H H C H
H C H C H double bond
am

-R

H C H C H
causes kink
H C H H C H in tail
-C

H C H C H
es

H C H
C H
y

C
Pr

H H H C H
op

H C H
ity

C H
C

H C H
saturated fatty acid
rs
w

H C H
unsaturated fatty acid
ie

ve

H
y
ev

op
ni

Figure 2.11: Structure of a saturated and an unsaturated fatty acid. Photographs of models are shown to the sides of the
R

structures. In the models, hydrogen is white, carbon is grey and oxygen is red.
e

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C
ge
head 3 hydrocarbon

w
tails

ie
id
H O H O

ev
br
am H C OH HO C H C O C

-R
O O
condensation
-C

s
H C OH HO C H C O C

es
O 3H2O O
y

Pr
op

H C OH HO C H C O C

ity
C

H H

rs
w

3 fatty acid molecules triglyceride

ie

ve
glycerol +
with hydrocarbon tails molecule

y
ev

op
ni
R

fatty acid fatty acid

C
ge

glycerol

glycerol
w
or, more simply fatty acid condensation fatty acid

ie
id

ev
br

fatty acid 3H2O fatty acid

am

-R
Key
glycerol fatty acid ester bond
-C

s
es

Figure 2.12: Formation of a triglyceride from glycerol and three fatty acid molecules.
y

Pr
op

ity
C

The –COOH group on the acid reacts with the –OH three hydrophobic fatty
rs
w

group on the alcohol to form the ester bond, –COO– . acid tails
ie

ve

This is a condensation reaction because water is formed

y
ev

as a product. The resulting ester can be converted back

op
ni

to acid and alcohol by the reverse reaction of adding

R

water, a reaction known as hydrolysis.

ge

glycerol
w
ie
id

Triglycerides Figure 2.13: Diagrammatic representation of a triglyceride

ev
br

The most common lipids are triglycerides (Figure 2.13). molecule.

am

-R

These are fats and oils. A glyceride is an ester formed

by a fatty acid combining with the alcohol glycerol. As
-C

you have seen, glycerol has three hydroxyl groups. Each Consequently, they are hydrophobic and do not mix
es

one is able to undergo a condensation reaction with freely with water molecules. Figure 2.13 shows a
y

simplified diagram of a triglyceride.

Pr

a fatty acid. When a triglyceride is made, as shown in

op

Figure 2.12, the final molecule contains three fatty acid

ity
C

tails and three ester bonds (‘tri’ means three). The tails
can vary in length, depending on the fatty acids used.
KEY WORD
rs
w
ie

triglyceride: a type of lipid formed when three

ve

Triglycerides are insoluble in water but are soluble

y

fatty acid molecules combine with glycerol, an

ev

in certain organic solvents such as ethanol. This is

op
ni

because the hydrocarbon tails are non-polar: they alcohol with three hydroxyl (−OH) groups
R

have no uneven distribution of electrical charge.

e

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ni
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ge
Functions of triglycerides The two remaining hydrocarbon tails are still

w
hydrophobic (Figure 2.15). This allows phospholipids

ie
id
Triglycerides make excellent energy stores because
to form a membrane around a cell; two rows of

ev
they are even richer in carbon–hydrogen bonds than

br
phospholipids are arranged with their hydrophilic
carbohydrates. A given mass of triglyceride will
am

-R
heads in the watery solutions on either side of the
therefore yield more energy on oxidation than the same
membrane and their hydrophobic tails forming a layer
mass of carbohydrate (it has a higher calorific value), an
-C

that is impermeable to hydrophilic substances. The

s
important advantage for a storage product.

es
biological significance of this will become apparent
Triglycerides are stored in a number of places in the
y

when you study membrane structure (Chapter 4).

Pr
op

human body, particularly just below the skin and

around the kidneys. Below the skin they also act as an

ity
C

insulator against loss of heat. Blubber, a triglyceride

rs
w

found in sea mammals such as whales, has a similar

ie

ve
function, as well as providing buoyancy. hydrophilic head two hydrophobic

y
containing fatty acid tails
ev

op
ni
An unusual role for triglycerides is as a metabolic source phosphate group
R

of water. When oxidised in respiration, triglycerides are

C
converted to carbon dioxide and water. The water may Figure 2.15: Diagrammatic representation of a
ge

w
be of importance in very dry habitats. For example, the phospholipid molecule. Compare this with Figure 2.13.

ie
id

desert kangaroo rat (Figure 2.14) never drinks water

ev
and survives on metabolic water from the triglyceride-
br

containing foods it eats.

am

PRACTICAL ACTIVITY 2.3

-R
-C

Testing for the presence of lipids

s
es

Lipids are insoluble in water, but soluble in ethanol

y

(alcohol). This fact is made use of in the emulsion

Pr
op

test for lipids.

ity
C

Procedure
rs
w

The substance that is thought to contain lipids

ie

ve

y
is shaken vigorously with some absolute ethanol
ev

op
ni

(ethanol with little or no water in it). This allows

R

any lipids in the substance to dissolve in the

C

ethanol. The ethanol is then poured into a tube

ge

containing water. If lipid is present, a cloudy

ie
id

white suspension is formed.

ev
br

Further information
am

-R

Figure 2.14: The desert kangaroo rat uses metabolism of

food to provide the water it needs. If there is no lipid present, the ethanol just mixes
-C

into the water. Light can pass straight through this

s
es

mixture, so it looks completely transparent. But

y

if there is lipid dissolved in the ethanol, it cannot

Phospholipids
Pr
op

remain dissolved when mixed with the water. The

lipid molecules form tiny droplets throughout the
ity
C

Phospholipids are a special type of lipid. Each

molecule has the unusual property of having one end liquid. This kind of mixture is called an emulsion.
rs
w

which is soluble in water. This is because one of the The droplets reflect and scatter light, making the
ie

ve

three fatty acid molecules is replaced by a phosphate liquid look white and cloudy.
y
ev

op
ni

group, which is polar and can therefore dissolve in (See Practical Investigation 2.1 in the Practical
water. The phosphate group is hydrophilic and makes
R

Workbook for additional information.)

C

the head of a phospholipid molecule hydrophilic.

e

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a
2.6 Proteins

w
R This group varies in

ie
different amino acids.

id
H O
It is known as the R group.

ev
Proteins are an extremely important class of N C C

br
macromolecule in living organisms. More than 50% of
am H OH

-R
the dry mass of most cells is protein. Proteins have many H
important functions: amino group carboxylic
-C

acid group

s
•

es
all enzymes are proteins
y

• proteins are essential components of cell b

Pr
op

H
membranes – their functions in membranes are H O

ity
C

discussed in Chapter 4 N C C
H OH

rs
w

• some hormones are proteins – for example, insulin

H
ie

ve
and glucagon

y
glycine
ev

op
ni
• the oxygen-carrying pigments haemoglobin and
R

myoglobin are proteins

U

Figure 2.16: a The general structure of an amino acid;

C
• antibodies, which attack and destroy invading b structure of the simplest amino acid, glycine, in which
ge

w
microorganisms, are proteins the R group is H, hydrogen.

ie
id

• collagen is a protein that adds strength to many

ev
br

animal tissues – for example, bone and the walls The R groups for the 20 different amino acids which
am

-R
occur in the proteins of living organisms are shown
of arteries
in Appendix 1. You do not need to remember these.
-C

• hair, nails and the surface layers of skin contain the Appendix 1 also shows the three-letter abbreviations for
s

protein keratin
es

the names of the amino acids. Many other amino acids

have been synthesised in laboratories.
y

• actin and myosin are the proteins responsible for

Pr
op

muscle contraction
ity
C

• proteins may be storage products – for example,

The peptide bond
rs
w

casein in milk and ovalbumin in egg white.

ie

ve

Despite their tremendous range of functions, all proteins Figure 2.17 shows how two amino acids can join
y
ev

are made from the same basic monomers. These are

op
ni

together. One loses a hydroxyl (–OH) group from its

amino acids. carboxylic acid group, while the other loses a hydrogen
R

atom from its amino group. This leaves a carbon atom

ge

of the first amino acid free to bond with the nitrogen

Amino acids
ie

atom of the second. The link is called a peptide bond.

id

The oxygen and two hydrogen atoms removed from

ev
br

Figure 2.16 shows the general structure of all amino

acids and the structure of glycine, the simplest amino the amino acids form a water molecule. You have seen
am

-R

acid. All amino acids have a central carbon atom which condensation reactions like this in the formation of
is bonded to an amino group, –NH2, and a carboxylic glycosidic bonds (Figure 2.5) and in the synthesis of
-C

acid group, –COOH. These two groups give amino acids triglycerides (Figure 2.12).
es

their name. The third component that is always bonded

y

Pr

to the carbon atom is a hydrogen atom. So, the only way

op

KEY WORD
in which amino acids differ from each other is in the
ity
C

fourth group of atoms bonded to the central carbon. peptide bond: the covalent bond joining
This is called the R group. neighbouring amino acids together in proteins; it
rs
w

is a C–N link between two amino acid molecules,

ie

ve

formed by a condensation reaction

ev

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R

C
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ni
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C
ge
amino acid amino acid dipeptide

w
ie
R R R O R

id
H O H O –H2O (condensation) H O

ev
br
N C C N C C N C C N C C
am H OH H OH +H2O (hydrolysis) H OH

-R
H H H H H
H2O
peptide bond
-C

s
es
Figure 2.17: Amino acids link together by the loss of a molecule of water to form a peptide bond.
y

Pr
op

The new molecule is made up of two linked amino acids

ity
C

Lys Phe Glu Arg Gln His

Ala Met
Ala
and is called a dipeptide. A molecule made up of many Ala 10 Asp

rs
w

Thr
amino acids linked together by peptide bonds is called 1 Glu
20
Ser
ie

ve
Lys Ser
a polypeptide. A polypeptide is another example of a Ser Ser
Ser Ala Ala Ser Thr

y
+H3N
ev

Asn
polymer and a macromolecule, like a polysaccharide. A

op
ni
30 Tyr 80
protein may have just one polypeptide chain or it may
R

Ser Tyr Ser Gln

U

Lys Met Met Cys IIe Ser Met Thr

Asp Thr Tyr

C
Ser Gln Asn
have two or more chains. Cys Cys
ge

Arg Arg Asn

Ser Gly Cys

w
Thr Glu 70 Thr
In living cells, protein synthesis takes place at ribosomes Asn Ser Lys Ala

ie
id

90 120 Gln
(Chapter 6). Leu Lys
Ser Ala Asp Phe Gly
Asn
Val
His Val Pro Val

ev
br

Thr Tyr 124 Val Tyr Pro Asn

Gly Asn
Proteins can be broken down to amino acids by Lys Pro O Glu
am

C Lys
breaking the peptide bonds. This is a hydrolysis reaction,
-R Asp Asn 110
Cys Gln
Cys O– Ser
involving the addition of water (Figure 2.17). It happens Arg
Ala
Ala
Cys
60
-C

Val
40 Cys Tyr
naturally in the stomach and small intestine during IIe
s
100 IIe Val
Lys Lys
Thr Thr His Ala
es

digestion of proteins in food. The amino acids released Pro Gln Ala Asn Lys
Gln
Val Val
y

are absorbed into the blood. Asn 50 Asp

Pr

Thr Phe Ala

op

Val His Glu Ser Leu

ity
C

Primary structure Figure 2.18: The primary structure of ribonuclease.

rs
w

Ribonuclease is an enzyme found in pancreatic juice, which

ie

ve

A polypeptide or protein molecule may contain several hydrolyses (digests) RNA (Chapter 6). Notice that at one end
y
ev

hundred amino acids linked into a long chain. The

op

of the amino acid chain there is an amino group (–NH3+), while

ni

particular amino acids contained in the chain, and the at the other end there is a carboxyl group (–COO– ). These
R

sequence in which they are joined, is called the primary are known as the amino and carboxyl ends or the N and C
ge

structure of the protein (Figure 2.18).

w

terminals respectively. Note the three-letter abbreviations for

ie

the amino acids. These are explained in Appendix 1.

id

ev
br

KEY WORDS
There are an enormous number of different possible
am

-R

polypeptide: a long chain of amino acids primary structures. A change in a single amino acid in
formed by condensation reactions between the a chain made up of thousands may completely alter the
-C

individual amino acids; proteins are made of one properties of the polypeptide or protein.
es

or more polypeptide chains; see peptide bond

y

Pr
op

primary structure: the sequence of amino acids Secondary structure

ity
C

in a polypeptide or protein
The amino acids in a polypeptide chain may have an
rs
w

secondary structure: the structure of a protein effect on each other even if they are not next to each
ie

ve

molecule resulting from the regular coiling or other in the primary sequence of amino acids. This is
y
ev

folding of the chain of amino acids (an α-helix or because the polypeptide chain can bend back on itself.
op
ni

β-pleated sheet) A polypeptide chain, or part of it, often coils into a

R

corkscrew shape forming a secondary structure called

e

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C
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an α-helix (Figure 2.19a). This secondary structure is temperatures and pH changes. As you will see, this has

w
due to hydrogen bonding between the oxygen of the important consequences for living organisms.

ie
id
C O group of one amino acid and the hydrogen of

ev
br
the –NH group of the amino acid four places ahead of
am KEY WORDS

-R
it. Each amino acid has an –NH and a C O group, and
Figure 2.19a shows that all these groups are involved in α-helix: a helical structure formed by a
-C

hydrogen bonding in the α-helix, holding the structure polypeptide chain, held in place by hydrogen

s
es
firmly in shape. Hydrogen bonding is a result of the bonds; an α-helix is an example of secondary
structure in a protein
y

polar characteristics of the C O and –NH groups.

Pr
op

Sometimes hydrogen bonding can result in a much β-pleated sheet: a loose, sheet-like structure

ity
C

looser, straighter shape than the α-helix, which is called a formed by hydrogen bonding between parallel
β-pleated sheet (Figure 2.19b). Although hydrogen bonds
rs
polypeptide chains; a β-pleated sheet is an
w

are strong enough to hold the α-helix and β-pleated example of secondary structure in a protein
ie

ve
sheet structures in shape, they are easily broken by high

y
ev

op
ni
R

C
C C C
ge

N H O N H

w
O C H N H

ie
N
id

H C C
N

ev
O
br

O C C C
C
O
am

C
-R
H O C N H
N
-C

H N H
N
s

O C O C C
C
es
y

Pr
op

8
ity
C

4
rs
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ie

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9 1
7 5
y
ev

3
op
ni
R

2
ge

6
w
ie
id

b
ev
br
am

-R
-C

s
es
y

Pr
op

ity
C

rs
w
ie

ve

hydrogen bond
y
ev

op
ni
R

Figure 2.19: Protein secondary structure. a Structure of the α-helix. The R groups are not shown. b Another common
C

secondary structure is the β-pleated sheet. Both of these structures are held in shape by hydrogen bonds between the
e

amino acids.
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ni
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C
ge

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ie
id

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br
am

-R
-C

s
es
y

Pr
op

ity
C

rs
w
ie

ve

y
ev

op
ni
R

C
Figure 2.20: Secondary and tertiary structure of lysozyme.
ge

w
α-helices are shown as blue coils, β-pleated sheets as green

ie
arrows, and random coils as red ribbons. The black zig-zags
id

are disulfide bonds.

ev
br

Figure 2.21: A computer graphic showing the secondary

am

-R
Some proteins or parts of proteins show no regular and tertiary structures of a myoglobin molecule. Myoglobin
is the substance which makes meat look red. It is found in
-C

arrangement at all. It all depends on which R groups are

s

present and what attractions occur between amino acids muscle, where it acts as an oxygen-storing molecule. The
es

in the chain. blue cylinders are α-helices and are linked by sections of
y

Pr

polypeptide chain which are random coils (shown in red).

op

In diagrams of protein structure, α-helices can be At the centre right is an iron-containing haem group.
ity
C

represented as coils or cylinders: β-pleated sheets as

arrows, and random coils as ribbons (Figures 2.20
rs

Figure 2.22 shows the four types of bond that help to

w

and 2.21). keep folded proteins in their precise shapes.

ie

ve

y
ev

• Hydrogen bonds can form between a wide variety

op
ni

of R groups. Hydrogen bonds are weak in isolation

R

Tertiary structure
C

but many together can form a strong structure.

ge

In many proteins, the secondary structure itself is coiled • Disulfide bonds form between two cysteine
ie
id

or folded. Figures 2.20 and 2.21 show the complex way molecules. Cysteine molecules contain sulfur atoms.
ev

in which secondary structure coils or folds to form the

br

The disulfide bond forms when the sulfur atoms of

tertiary structure of a protein. The figures show different neighbouring cysteines join together with a covalent
am

-R

ways in which the structures can be represented by bond. This is a strong bond. (Can you spot the four
diagrams. At first sight, the lysozyme and myoglobin disulfide bonds in ribonuclease in Figure 2.18?)
-C

molecules in these figures look like disorganised tangles,

es

but this is not so. The shape of the molecules is very • Ionic bonds form between R groups containing
y

amino and carboxyl groups. (Which amino acids have

Pr

precise, and the molecules are held in these exact shapes by

op

bonds between amino acids in different parts of the chain. R groups containing amino or carboxyl groups?)
ity
C

• Hydrophobic interactions occur between R groups

that are non-polar. Such R groups are hydrophobic
rs
w

KEY WORD
so tend to avoid water if possible. If the protein is in
ie

ve

tertiary structure: the compact structure of a typical watery environment inside the cell, then the
ev

op
ni

a protein molecule resulting from the three- hydrophobic R groups will tend to come together,
R

dimensional coiling of the chain of amino acids excluding water. The overall shape of many proteins
C

is affected by such hydrophobic interactions.

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a Hydrogen bonds form between strongly polar groups –

w
for example, –NH–, –CO– and –OH groups.

ie
id

ev
br
am polypeptide chain

-R
-C

δ+ δ−

s
N H O C

es
a
y

hydrogen bond

Pr
op

ity
C

b Disulfide bonds form between cysteine molecules. They are

rs
w

strong covalent bonds. They can be broken by reducing agents.

ie

ve

y
ev

op
ni

S
R

C
−2H (oxidation) S
H
ge

w
H
S

ie
+2H (reduction)
id

S b

ev
br

disulfide bond
am

-R
c Ionic bonds form between ionised amino (NH3+) groups and An oxygen molecule can
-C

bond with the iron atom.

s

ionised carboxylic acid (COO −) groups. They can be broken by

es

pH changes.
y

Pr
op

Key
ity
C

NH3+
rs
w

iron carbon nitrogen oxygen

ie

ionic bond
ve

COO −
y
ev

op
ni

c
R

C
ge

β chain (2 present)
w

d Weak hydrophobic interactions occur between non-polar

ie
id

R groups. Although the interactions are weak, the groups tend

ev
br

to stay together because they are repelled by the watery

environment around them.
am

-R

α chain (2 present)
-C

haem group
es

R two non-polar R
y

Pr

R groups Figure 2.23: Haemoglobin. a Each haemoglobin

op

molecule contains four polypeptide chains. The two

ity
C

α chains are shown in purple and blue, and the two

β chains in brown and orange. Each polypeptide
rs
w

Figure 2.22: The four types of bond which are important in chain contains a haem group, shown in yellow and
ie

ve

protein tertiary structure: a hydrogen bonds, which are also red. b The haem group contains an iron atom, which
ev

op
ni

important in secondary structure; b disulfide bonds; c ionic can bond reversibly with an oxygen molecule. c The
R

bonds; d hydrophobic interactions. complete haemoglobin molecule is nearly spherical.

C
e

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-R

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ni
U

C
ge
The R groups are typically orientated towards the Many globular proteins have roles in metabolic reactions.

w
centre of the proteins, facing away from the outside Their precise shape is the key to their functioning.

ie
id
watery environment, with the hydrophilic R groups Enzymes, for example, are globular proteins.

ev
br
surrounding them and pointing outwards and in
am Many other protein molecules do not curl up into a

-R
contact with the watery environment.
ball, but form long strands. These are known as fibrous
proteins. Fibrous proteins are not usually soluble in
-C

s
Quaternary structure water and most have structural roles. For example, the

es
fibrous protein keratin forms hair, nails and the outer
y

Pr
Many protein molecules are made up of two or more layers of skin, making these structures waterproof.
op

polypeptide chains. The overall structure formed by Another example of a fibrous protein is collagen.

ity
C

the different polypeptide chains is called the quaternary

structure of the protein. Haemoglobin is an example of

rs
Haemoglobin – a globular protein
w

a protein with a quaternary structure. A molecule of

ie

ve
haemoglobin has four polypeptide chains (Figure 2.23). Haemoglobin is the oxygen-carrying pigment found in

y
ev

red blood cells. It is a globular protein. You have seen

op
ni

The polypeptide chains in quaternary structures are held that it is made up of four polypeptide chains, so it has
R

C
together by the same four types of bond as in tertiary a quaternary structure. Each chain is a protein known
ge

structures. as globin. Globin is related to myoglobin and so has a

w
very similar tertiary structure (Figures 2.21 and 2.23).

ie
id

There are many types of globin – two types are used to

Globular and fibrous proteins
ev
br

make haemoglobin, and these are known as α-globin

am

-R (alpha-globin) and β-globin (beta-globin). Two of the

A protein whose molecules curl up into a ball shape,
such as myoglobin or haemoglobin, is known as a haemoglobin chains, called α chains, are made from
-C

α-globin, and the other two chains, called β chains, are

s

globular protein. Globular proteins usually curl up so

es

that their non-polar, hydrophobic R groups point into made from β-globin.
y

the centre of the molecule, away from their watery

Pr

The haemoglobin molecule is nearly spherical

op

surroundings. Water molecules are excluded from (Figure 2.23). The four polypeptide chains pack closely
ity

the centre of the folded protein molecule. The polar,

C

together. Their hydrophobic R groups point in towards

hydrophilic R groups remain on the outside of the the centre of the molecule, and their hydrophilic ones
rs
w

molecule. Globular proteins, therefore, are usually point outwards.

ie

ve

soluble, because water molecules cluster around their

y
ev

outward-pointing hydrophilic R groups (Figure 2.24). The interactions between the hydrophobic R groups
op
ni

inside the molecule are important in holding it in its

R

amino acid with correct three-dimensional shape. The outward-pointing

ge

hydrophilic R group hydrophilic R groups on the surface of the molecule are

w
ie

amino acid with

id

hydrophobic
ev

KEY WORDS
br

R group
am

-R

quaternary structure: the three-dimensional

arrangement of two or more polypeptides, or of a
-C

polypeptide and a non-protein component such

es

as haem, in a protein molecule

y

Pr

haemoglobin: the red pigment found in red

op

blood cells, whose molecules contain four iron

ity
C

atoms within a globular protein made up of four

polypeptides; it combines reversibly with oxygen
rs
w

Figure 2.24: A section through part of a globular protein

ie

ve

globular protein: a protein whose molecules are

y

molecule. The polypeptide chain coils up with hydrophilic folded into a relatively spherical shape, often has
ev

op
ni

R groups outside and hydrophobic R groups inside. This physiological roles and is often water-soluble and
R

arrangement makes the molecule soluble. metabolically active, e.g. insulin, haemoglobin
C
e

and enzymes
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-R

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2 Biological molecules

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important in maintaining its solubility. In the genetic It is the haem group which is responsible for the colour

w
condition known as sickle cell anaemia, one amino acid of haemoglobin. This colour changes depending

ie
id
on the surface of the β chain is replaced with a different on whether or not the iron atoms are combined

ev
br
amino acid. The correct amino acid is glutamic acid,
am with oxygen. If they are, the molecule is known as

-R
which is polar. The substitute is valine, which is non- oxyhaemoglobin and is bright red. If not, the colour is a
polar. Having a non-polar R group on the outside of darker, more bluish red.
-C

the molecule makes the haemoglobin much less soluble,

s
es
and causes the unpleasant and dangerous symptoms Collagen – a fibrous protein
y

associated with sickle cell anaemia (Figure 2.25).

Pr
Collagen is the most common protein found in animals,
op

a
making up 25% of the total protein in mammals. It is

ity
C

an insoluble fibrous protein (Figure 2.26) found in skin,

rs
tendons, cartilage, bones, teeth and the walls of blood
w

vessels. It is an important structural protein in almost

ie

ve

y
all animals.
ev

op
ni
R

KEY WORDS

C
ge

w
sickle cell anaemia: a genetic disease caused by

ie
id

a faulty gene coding for haemoglobin, in which

ev
br

haemoglobin tends to precipitate when oxygen

concentrations are low
am

-R
b collagen: the main structural protein of animals;
-C

known as ‘white fibres’, the fundamental unit of

es

the fibre consists of three helical polypeptide

y

chains wound around each other, forming a

Pr
op

‘triple helix’ with high tensile strength

ity
C

fibrous protein: a protein whose molecules have

rs
w

a relatively long, thin structure that is generally

ie

ve

insoluble and metabolically inactive, and whose

y
ev

function is usually structural, e.g. keratin and

op
ni

collagen
R

C
ge

Figure 2.25: a Scanning electron micrograph of human red A collagen molecule consists of three polypeptide chains,
ie
id

blood cells (×3300 ). Each cell contains about 250 million each in the shape of a helix (Figure 2.26b). (This is not
ev
br

haemoglobin molecules. b Scanning electron micrograph of an α-helix – it is not as tightly wound.) These three
red blood cells from a person with sickle cell anaemia. You helical polypeptides are wound around each other,
am

-R

can see a normal cell and three sickled cells (×3300 ). forming a three-stranded ‘rope’ or ‘triple helix’. The three
strands are held together by hydrogen bonds and some
-C

Each of the four polypeptide chains of haemoglobin covalent bonds. Almost every third amino acid in each
es

contains a haem group (Figure 2.23b). A group like this, polypeptide is glycine, the smallest amino acid. Glycine
y

Pr

is found on the insides of the strands and its small size

op

which is an important and permanent part of a protein

molecule, but is not made of amino acids, is called a allows the three strands to lie close together and so form
ity
C

prosthetic group. a tight coil. Any other amino acid would be too large.
rs
w

Each haem group contains an iron atom. One oxygen Each complete, three-stranded molecule of collagen
ie

ve

molecule (O2) can bind with each iron atom. So a interacts with other collagen molecules running parallel
y
ev

complete haemoglobin molecule, with four haem groups, to it. Covalent bonds form between the R groups of
op
ni

can carry four oxygen molecules (eight oxygen atoms) at amino acids lying next to each other. These cross-links
R

a time. hold many collagen molecules side by side, forming

e

fibrils. The ends of the parallel molecules are staggered;

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-R

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a b c

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ev
br
am 3

-R
E
N

2
G LY C I

1 helix with
-C

three amino

s
es
acids per turn
NE
y

Pr
op

NI
A
AL

ity
C

rs
w

INE
ie

ve
OL

y
ev

PR

op
ni
R

C
E
G LY C I N

ge

w
Three helices wind together to

ie
id

form a collagen molecule. These

ev
br

strands are held together by

hydrogen bonds and some
am

-R
covalent bonds. Many of these triple helices lie side
The polypeptides which make by side, linked to each other by
-C

up a collagen molecule are in covalent cross-links between the

s
es

the shape of a stretched-out side chains of amino acids near the

helix. Every third amino acid is ends of the polypeptides. Notice
y

Pr
op

glycine. that these cross-links are out of

step with each other; this gives
ity
C

d collagen greater strength.

rs
w

e
ie

ve

y
ev

op
ni
R

C
ge

w
ie
id

ev
br
am

-R
-C

A scanning electron micrograph of collagen fibrils A scanning electron micrograph of human

s
es

(× 17 000). Each fibril is made up of many triple collagen fibres (×2000). Each fibre is made
helices lying parallel with one another. The banded up of many fibrils lying side by side. These
y

Pr
op

appearance is caused by the regular way in which fibres are large enough to be seen with an
these helices are arranged, with the staggered gaps ordinary light microscope.
ity
C

between the molecules (shown in c) appearing

darker.
rs
w
ie

ve

Figure 2.26: Collagen. The diagrams and photographs begin with the very small and work up to the not-so-small. Thus, three
ev

op
ni

polypeptide chains like the one shown in a make up a collagen molecule, shown in b; many collagen molecules make up a
R

fibril, shown in c and d; many fibrils make up a fibre, shown in e.

C
e

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2 Biological molecules

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if they were not, there would be a weak spot running cross-sectional area, about one-quarter the tensile

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right across the collagen fibril. Finally, many fibrils lie strength of mild steel.

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alongside each other, forming strong bundles called

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Collagen fibres are lined up in different structures
fibres. Note that many collagen molecules make up one
am according to the forces they must withstand. In tendons,

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collagen fibre.
they line up in parallel bundles along the length of
The advantage of collagen is that it is flexible but at the the tendon, in the direction of tension. In skin, they
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same time has tremendous tensile strength. High tensile may form layers, with the fibres running in different

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strength means it can withstand large pulling forces directions in the different layers, like cellulose in cell
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without stretching or breaking. The human Achilles walls. In this way, they resist tensile (pulling) forces
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tendon, which is almost pure collagen fibres, can from many directions.

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withstand a pulling force of 300 N per mm2 of

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PRACTICAL ACTIVITY 2.4

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Testing for the presence of proteins solution and the hydroxide ready mixed. To stop the
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copper ions reacting with the hydroxide ions and
All proteins have peptide bonds, containing
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forming a precipitate, this ready-mixed reagent also

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nitrogen atoms. The nitrogen forms a purple
contains sodium potassium tartrate or sodium citrate.

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complex with copper(II) ions and this forms the basis

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of the biuret test. Procedure

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The reagent used for this test is called biuret The biuret reagent is added to the solution to be
reagent. You can use it as two separate solutions: tested. No heating is required. A purple colour
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a dilute solution of potassium hydroxide or sodium indicates that protein is present. The colour
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hydroxide, and a dilute solution of copper(II) sulfate. develops slowly over several minutes.
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Alternatively, you can use a ready-made biuret

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reagent that contains both the copper(II) sulfate (See Practical Investigation 2.1 in the Practical
Workbook for additional information.)
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Questions
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KEY WORD
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6 State three similarities and three differences between

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biuret test: a test for the presence of amine

cellulose and collagen.
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groups and thus for the presence of protein;

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7 Copy Table 2.1. Fill in the blanks in the second biuret reagent is added to the unknown
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column of the table using the words below: substance, and a change from pale blue to
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hydrophilic haemoglobin ionic bond purple indicates the presence of protein

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hydrophobic disaccharide disulfide bond

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Try with a partner to make a similar table with Description Word/term

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different statements based on the topics in this term for water-hating

chapter. Try it out on other students.
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broken by a reduction reaction

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8 ‘The protein-folding problem’ box at the beginning

of this chapter discussed how scientists are trying formed by a condensation reaction
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to predict the final shapes of proteins from a characteristic of globular proteins

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knowledge of their primary structures. What has two alpha chains and two
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information about amino acids and proteins would beta chains

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be relevant to feed into a computer program trying

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to make such predictions? can be broken by pH changes

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Table 2.1: Table for Question 7.

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positively charged water molecule

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2.7 Water ion (cation) e.g. Na+

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negatively

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Water is arguably the most important biochemical of charged
all. Without water, life would not exist on this planet.
am ion (anion)

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It is important for two reasons. First, it is a major e.g. Cl−
component of cells, typically forming between 70% and + −
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95% of the mass of the cell. You are about 60% water.

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Second, it provides an environment for those organisms
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that live in water. Three-quarters of the planet is covered
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in water.
oxygen (2δ −) hydrogen (δ+)

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Although it is a simple molecule, water has some faces the ion faces the ion

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surprising properties. For example, such a small

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molecule would exist as a gas at normal Earth Figure 2.27: Distribution of water molecules around ions in

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temperatures were it not for its special property of a solution. Note which atoms of the water molecules face

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hydrogen bonding to other water molecules, discussed the ions.

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earlier. Also, because water is a liquid, it provides a
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medium for molecules and ions to mix in, and hence a

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medium in which life can evolve.

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High specific heat capacity
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The hydrogen bonding of water molecules makes it

more difficult to separate the molecules and thus affects The heat capacity of a substance is the amount of heat
am

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the physical properties of water. For example, the energy required to raise its temperature by a given amount. The
needed to break the hydrogen bonds makes it relatively specific heat capacity of water is the amount of heat
-C

difficult to convert water from a liquid to a gas. It is energy required to raise the temperature of 1 kg of water
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more difficult than for similar compounds which lack by 1 °C.

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hydrogen bonds, such as hydrogen sulfide (H2S), which

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Water has a relatively high specific heat capacity. In

is a gas at normal air temperatures. order for the temperature of a liquid to be raised, the
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molecules must gain energy and consequently move

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about more rapidly. The hydrogen bonds that tend

Water as a solvent
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to make water molecules stick to each other make it

ve

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more difficult for the molecules to move about freely.
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Water is an excellent solvent for ions and polar molecules

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(molecules with an uneven charge distribution, such The bonds must be broken to allow free movement.
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This explains why more energy is needed to raise

C

as sugars and glycerol). This is because the water

the temperature of water than would be the case if
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molecules are attracted to the ions and polar molecules

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and therefore collect around them and separate them there were no hydrogen bonds. Hydrogen bonding, in
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(Figure 2.27). This is what happens when a chemical effect, allows water to store more energy for a given
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dissolves in water. Once a chemical is in solution, its temperature rise than would otherwise be possible.
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molecules or ions are free to move about and react with The high specific heat capacity of water has important
other chemicals. Most processes in living organisms take biological implications because it makes water more
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place in solution in this way. The fact that molecules and

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resistant to changes in temperature. This means that

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ions dissolve in water also makes it ideal as a transport the temperature within cells and within the bodies of
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medium, for example, in the blood and lymphatic organisms (which have a high proportion of water) tends
Pr
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systems in animals, and in xylem and phloem in plants. to be more constant than that of the air around them.
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By contrast, non-polar molecules such as lipids are As a result, biochemical reactions operate at relatively
constant rates and are less likely to be adversely affected
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insoluble in water and, if surrounded by water, tend

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to be pushed together by the water, since the water by extremes of temperature. It also means that large
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bodies of water such as lakes and oceans are slow to

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molecules are attracted to each other. This is important,

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for example, in hydrophobic interactions in protein change temperature as air temperature changes. As
a result, lakes and oceans provide stable habitats for
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structure and in membrane structure (Chapter 4), and it

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increases the stability of proteins and membranes. aquatic organisms.

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2 Biological molecules

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High latent heat of vaporisation It can also be important in cooling leaves during

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transpiration.

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The latent heat of vaporisation is a measure of the

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The reverse is true when water changes from liquid to

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heat energy needed to vaporise a liquid (cause it to
am solid ice. This time the water molecules must lose a

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evaporate), changing it from a liquid to a gas. In the
relatively large amount of energy, making it less likely
case of water, it involves the change from liquid water to
that water will freeze. This is an advantage for aquatic
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water vapour.

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organisms. It also makes it less likely that the bodies

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Water has a relatively high latent heat of vaporisation. of living organisms, which have a high water content,
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This is a consequence of its high specific heat capacity. will freeze.
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The fact that water molecules tend to stick to each

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other by hydrogen bonds means that relatively large

amounts of energy are needed for vaporisation to Question
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occur, because hydrogen bonds have to be broken

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before molecules can escape as a gas. The energy 9 State the property of water that allows each of the

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following (a, b and c) to take place. Explain the

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transferred to water molecules during vaporisation
importance of a, b and c:
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results in a corresponding loss of energy from their

C
surroundings, which therefore cool down. This a the cooling of skin during sweating
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is biologically important because it means that b the transport of glucose and ions in a mammal

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living organisms can use evaporation as a cooling c much smaller temperature fluctuations in lakes

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mechanism, as in sweating or panting in mammals. A
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and oceans than in terrestrial (land-based)

large amount of heat energy can be lost for relatively
am

habitats.
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little loss of water, reducing the risk of dehydration.
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REFLECTION
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• Explain the importance of simple biochemical understanding of biochemistry? What does this
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molecules such as sugars, amino acids, organic show you about the way you like to learn?
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bases, fatty acids and glycerol in the evolution

Final reflection
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of life.
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• Water and carbon are important for life. How Discuss with a friend which, if any, parts of
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would you justify this statement? Chapter 2 you need to:

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• read through again to make sure you really

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Personal reflection questions

understand
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While studying this chapter, what activities

• seek more guidance on, even after going over
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have been particularly useful in improving your

it again.
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SUMMARY

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The larger biological molecules are made from smaller molecules. The smaller molecules are joined together by
condensation reactions. Condensation involves removal of water. The reverse process, adding water, is called
am

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hydrolysis and is used to break the large molecules back down into smaller molecules. Polysaccharides are
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made from monosaccharides, proteins (polypeptides) from amino acids, lipids from fatty acids and glycerol.

s
Polysaccharides and proteins are formed from repeating identical or similar subunits called monomers. They

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are, therefore, polymers. These build up into giant molecules called macromolecules.
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Carbohydrates have the general formula Cx(H2O)y and include monosaccharides, disaccharides and

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polysaccharides. Monosaccharides are joined together by glycosidic bonds to make disaccharides and
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polysaccharides. Monosaccharides (e.g. glucose) and disaccharides (e.g. sucrose) are very water-soluble and

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are known as sugars. They are important energy sources in cells and also important building blocks for larger
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molecules like polysaccharides.

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Monosaccharides may have straight-chain or ring structures and may exist in different isomeric forms such as
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α-glucose and β-glucose.

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Benedict’s reagent can be used to test for reducing and non-reducing sugars. The test is semi-quantitative.

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Polysaccharides include starch, glycogen and cellulose. Starch is an energy storage compound in plants. Starch

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is made up of two types of molecule, amylose and amylopectin, both made from α-glucose. Amylose is an
unbranching molecule, whereas amylopectin has a branching structure.
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‘Iodine solution’ can be used to test for starch.
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Glycogen is an energy storage compound in animals. It is made from α-glucose. Its structure is similar to that
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of amylopectin but with more branching. Cellulose is a polymer of β-glucose molecules. The molecules are
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grouped together by hydrogen bonding to form mechanically strong fibres with high tensile strength that are
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found in plant cell walls.

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Lipids are a diverse group of chemicals, the most common of which are triglycerides (fats and oils).
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Triglycerides are made by condensation between three fatty acid molecules and glycerol. Ester bonds join
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the fatty acids to the glycerol. Triglycerides are hydrophobic and do not mix with water. They act as energy
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storage compounds, as well as having other functions such as insulation and buoyancy in marine mammals.
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Phospholipids have a hydrophilic phosphate head and two hydrophobic fatty acid tails. This is important in the
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formation of membranes.
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The emulsion test can be used to test for lipids.

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Proteins are long chains of amino acids which fold into precise shapes. Amino acids are joined together by
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peptide bonds.
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Proteins have up to four levels of structure known as primary, secondary, tertiary and quaternary structures.
The primary structure is the sequence of amino acids in a protein. This largely determines the way that it folds
-C

and hence its three-dimensional shape and function.

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Secondary structure is a result of hydrogen bonding between the amino acids. Examples of secondary structure
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are the α-helix and the β-pleated sheet. Further folding of proteins produces the tertiary structure. Often, a
protein is made from more than one polypeptide chain. The association between the different chains is the
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quaternary structure of the protein. Tertiary and quaternary structures are very precise and are held in place by
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hydrogen bonds, disulfide bonds (which are covalent), ionic bonds and hydrophobic interactions.
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CONTINUED

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Proteins may be globular or fibrous. A molecule of a globular protein – for example, haemoglobin – is roughly
spherical. Most globular proteins are soluble and have physiological roles. Haemoglobin contains a non-protein
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(prosthetic) group, the haem group, which contains iron. This combines with oxygen. Molecules of a fibrous protein
– for example, collagen – form long strands. Fibrous proteins are usually insoluble and have a structural role.
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Collagen has high tensile strength and is the most common animal protein, being found in a wide range of tissues.

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Biuret reagent can be used to test for proteins.

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Hydrogen bonding between water molecules gives water unusual properties.

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Water is liquid at most temperatures on the Earth’s surface. It has a high specific heat capacity, which makes

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liquid water relatively resistant to changes in temperature. Water acts as a solvent for ions and polar molecules,
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and causes non-polar molecules to group together. Water has a relatively high latent heat of vaporisation,

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meaning that evaporation has a strong cooling effect.

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EXAM-STYLE QUESTIONS

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1 Which term describes both collagen and haemoglobin?

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A enzymes
B fibrous proteins
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C globular proteins
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D macromolecules [1]
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2 What type of chemical reaction is involved in the formation of disulfide bonds?

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A condensation
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B hydrolysis
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C oxidation
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D reduction [1]
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3 Which diagram best represents the arrangement of water molecules around

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sodium (Na+) and chloride (Cl− ) ions in solution? [1]

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Na+ Na+ Na+ Na+

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Cl− Cl− Cl− Cl−

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A B C D
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Chapter 3
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Enzymes ity
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LEARNING INTENTIONS
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In this chapter you will learn how to:

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• state what enzymes are

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• explain the mode of action of enzymes

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• investigate the progress of enzyme-controlled reactions

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• outline the use of a colorimeter for measuring the progress of enzyme-catalysed reactions
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• investigate and explain the effect of temperature, pH, enzyme concentration and substrate concentration
ie

on the rate of enzyme-catalysed reactions

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• use Vmax and Km to compare the affinity of different enzymes for their substrates
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• explain the effects of reversible inhibitors, both competitive and non-competitive, on enzyme activity
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• state the advantages of using immobilised enzymes.

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3 Enzymes

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BEFORE YOU START

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• Enzymes are catalysts. Check your understanding of the term catalyst by stating two important

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properties of catalysts.
am

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• Enzymes are proteins. You studied proteins in Chapter 2. Discuss what properties of proteins might
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make them suitable to act as catalysts in living cells.

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THE BEST MEANS OF DEFENCE IS ATTACK

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If you are a beetle and you are about to be eaten into quinone. The reactions are violent and release

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by a predator such as a spider or a frog, how do a great deal of heat, vaporising about 20% of the
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you escape? The bombardier beetle has evolved resulting liquid. Within a fraction of a second,

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a spectacular and successful strategy (Figure 3.1). a boiling, stinking mixture of gas and liquid is

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It makes use of the very high speeds of enzyme- explosively released through an outlet valve.
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controlled reactions. When threatened by a
Question for discussion
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predator, the beetle uses the tip of its abdomen to

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squirt a boiling hot chemical spray at its attacker. It could be argued that carrying out research into

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the defence mechanism of the bombadier beetle

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The release of the spray is accompanied by a loud is a waste of time and money. Can you justify
popping sound. The beetle can swivel the tip of its the research?
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abdomen to spray accurately in almost any direction.
With the predator reeling from this surprise attack,
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the beetle escapes. a b

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How are enzymes involved? Inside the beetle’s

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abdomen is a chemical mixing chamber into which

hydrogen peroxide and hydroquinone are released.
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The chamber contains two enzymes, catalase and

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peroxidase. These enzymes speed up the reactions

Figure 3.1: a A bombardier beetle sprays a boiling
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they catalyse by several million times. Hydrogen

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chemical spray at an annoying pair of forceps;
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peroxide is broken down into oxygen and water

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b abdominal organs generating the spray.

and the oxygen is used to oxidise the hydroquinone
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Question
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3.1 What is an enzyme?

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1 A student investigated the effect of several different

An enzyme is a biological catalyst. It is biological
catalysts on the rate of decomposition of hydrogen
-C

because all enzymes are proteins. It is a catalyst because

s

peroxide to water and oxygen. The speed of the

it speeds up a chemical reaction but remains unchanged
es

reaction was judged by how ‘fizzy’ or frothy the

at the end of the reaction.
y

contents of the tube became when the catalyst was

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The following points are also important. added (oxygen is a product of the reaction and
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forms bubbles).
• Enzymes are globular proteins. They fold up into
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precise shapes.
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• Almost all metabolic reactions which take place in KEY WORD

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living organisms are catalysed by enzymes; enzymes

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enzyme: a protein produced by a living organism

are therefore essential for life.
R

that acts as a biological catalyst in a chemical

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• Many enzyme names end in –ase; for example, reaction by reducing activation energy
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amylase and ATPase.

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The student used iron filings and manganese the lock-and-key hypothesis. The substrate is the key

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dioxide as inorganic catalysts. They also used a whose shape fits the lock of the enzyme. The substrate

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commercial preparation of the enzyme catalase is held in place by temporary bonds which form

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and pieces of liver and pieces of potato tuber, both
am between the substrate and some of the R groups of

-R
of which contain catalase. Catalase catalyses the the enzyme’s amino acids. This combined structure is
decomposition of hydrogen peroxide. termed the enzyme–substrate complex.
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Results showed: Each enzyme will act on only one type of substrate

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• catalase, liver and potato were much more molecule. This is because the shape of the active site
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efficient than the inorganic catalysts will only allow one shape of molecule to fit. The enzyme
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• pure catalase was more efficient than the liver is said to be specific for this substrate. You can also

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and potato describe the enzyme as showing specificity.

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• liver was more efficient than potato In 1959 the lock-and-key hypothesis was modified in
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• ground-up liver was more efficient than pieces the light of evidence that enzyme molecules are more

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of liver. flexible than is suggested by a rigid lock and key. The

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modern hypothesis for enzyme action is known as the

R

Try to explain the student’s results.

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induced-fit hypothesis. It is basically the same as the
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lock-and-key hypothesis, but adds the idea that the

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Intracellular and extracellular enzyme, and sometimes the substrate, can change shape

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slightly as the substrate molecule enters the enzyme, in

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enzymes order to ensure a perfect fit. This makes the catalysis

am

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Not all enzymes work inside cells. Those that do are
An enzyme may catalyse a reaction in which the
-C

described as intracellular. Enzymes that are secreted

s

by cells and catalyse reactions outside cells are substrate molecule is split into two or more molecules,
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described as extracellular. Digestive enzymes in the as shown in Figure 3.2. Alternatively, it may catalyse
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the joining together of two molecules, as when making

op

gut are extracellular enzymes. Some organisms secrete

enzymes outside their bodies. Fungi, for example, a dipeptide from two amino acids. A simplified diagram
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often do this in order to digest the food on which they is shown in Figure 3.3. This diagram also shows the
enzyme–product complex which is briefly formed before
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are growing.
release of the product. When the reaction is complete,
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the product or products leave the active site. The enzyme

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is unchanged by this process, so it is now available to

3.2 Mode of action
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receive another substrate molecule.

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of enzymes
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KEY WORDS
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The lock-and-key hypothesis active site: an area on an enzyme molecule

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where the substrate can bind

and the induced-fit hypothesis lock-and-key hypothesis: a hypothesis for
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Like all globular proteins, enzyme molecules are coiled enzyme action; the substrate is a complementary
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into a precise three-dimensional shape. Hydrophilic shape to the active site of the enzyme, and fits
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exactly into the site; the enzyme shows specificity

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R groups (side-chains) on the outside of the molecule

make them soluble in the water in the cytoplasm. for the substrate
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Enzyme molecules have a special feature called an induced-fit hypothesis: a hypothesis for enzyme
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active site (Figure 3.2). The active site of an enzyme action; the substrate is a complementary shape
ie

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is a region to which another molecule (or molecules) to the active site of the enzyme, but not an exact
y
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can bind. This molecule is the substrate of the enzyme.

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fit – the enzyme, or sometimes the substrate, can

The shape of the active site allows the substrate to fit
R

change shape slightly to ensure a perfect fit, but

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perfectly. The idea that the enzyme has a particular it is still described as showing specificity
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shape into which the substrate fits exactly is known as

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3 Enzymes

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substrate (key) products

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active site enzyme–substrate complex

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enzyme (lock)

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a An enzyme has a cleft in its b Random movement of enzyme and c The interaction of the substrate with the
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surface, called the active site. substrate brings the substrate into active site breaks the substrate apart.

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The substrate molecule has a the active site. An enzyme–substrate An enzyme–product complex is briefly

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complementary shape. complex is temporarily formed. The formed, before the two product
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R groups of the amino acids in the molecules leave the active site, leaving

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active site interact with the substrate. the enzyme molecule unchanged and
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ready to bind with another

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substrate molecule.

ev
br

Figure 3.2: How an enzyme catalyses the breakdown of a substrate molecule into two product molecules.
am

-R
-C

enzyme The rate of the overall reaction can be very high.

s

substrates
es

(lock) (keys) A molecule of the enzyme catalase, for example, can

y

bind with hydrogen peroxide molecules, split them into

Pr
op

water and oxygen, and release the products at a rate of

10 million molecules per second.
ity
C

rs

The example of lysozyme

w
ie

ve

The interaction between the substrate and the active

y
ev

site, including the slight change in shape of the enzyme

op
ni

(induced fit) which results from the binding of the

R

enzyme–substrate
C

substrate, is clearly shown by the enzyme lysozyme.

complex
ge

Lysozyme is found in tears, saliva and other secretions.

w

It acts as a natural defence against bacteria. It does

ie
id

this by breaking the polysaccharide chains that form

ev
br

the cell walls of the bacteria. The tertiary structure

am

-R

of the enzyme has already been shown in Figure 2.20.

enzyme–product Figure 3.4 shows how the polysaccharide chains in the
-C

complex
bacterial cell wall are broken down in the active site of
s
es

product lysozyme.
y

Pr
op

Enzymes reduce activation

ity
C

rs

energy
w
ie

ve

Enzymes increase the rate at which chemical reactions

ev

op
ni

Figure 3.3: A simplified diagram of enzyme function. Note occur. Without enzymes, most of the reactions that
R

that in this example the enzyme is catalysing the joining occur in living cells would occur so slowly that life
C

together of two molecules. could not exist.

e

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-R

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ni
U

C
ge
a substrate One way of providing the extra energy needed is to heat

w
enzyme–substrate the substances. For example, in the Benedict’s test for

ie
id
enzyme complex reducing sugar you need to heat the Benedict’s reagent

ev
br
am and sugar solution together before they will react.

-R
Enzymes avoid this problem because they decrease
the activation energy of the reactions they catalyse
-C

s
(Figure 3.5b). They do this by holding the substrate or

es
substrates in such a way that their molecules can react
y

Pr
more easily. As a result, reactions catalysed by enzymes
op

products enzyme–product take place rapidly at a much lower temperature than

ity
C

enzyme complex they otherwise would.

rs
w

a To change a substrate into a

ie

ve
product, the energy of the

y
ev

op
ni
substrate must be briefly raised
by an amount known as the
R

C
activation energy. This can be
ge

done by heating the substrate.

w
Energy
b

ie
id

activation energy

ev
br

substrate
am

-R
-C

products
s
es
y

Progress of reaction
Pr
op

ity
C

b When a substrate binds to the

active site of an enzyme, the
rs
w

shape of its molecule is slightly

ie

ve

changed. This makes it easier

y
ev

op
ni

to change the substrate into a

product; the activation energy
R

Energy

is lower.
ge

activation energy
w
ie

substrate
id

ev
br
am

products
-R

Figure 3.4: Lysozyme breaking a polysaccharide chain. This

-C

is a hydrolysis reaction. a Diagram showing the formation

s

Progress of reaction
of enzyme–substrate and enzyme–product complexes, and
es

release of the products. b Space-filling model showing the

y

Figure 3.5: Activation energy: a without enzyme; b with

Pr
op

substrate in the active site of the enzyme. The substrate is

enzyme.
a polysaccharide chain which slides neatly into the groove
ity
C

(active site) and is split by the enzyme. Many such chains

rs
w

give the bacterial cell wall rigidity. When the chains are
KEY WORD
ie

ve

broken, the wall loses its rigidity and the bacterial cell
y
ev

explodes as a result of osmosis. activation energy: the energy that must be

op
ni

provided to make a reaction take place; enzymes

R

In many chemical reactions, the substrate is not

C

reduce the activation energy required for a

converted to a product unless some energy is added.
e

substrate to change into a product

w
g

This energy is called activation energy (Figure 3.5a).

ie
id

ev
br
am

-R

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3 Enzymes

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ni
U

C
ge
The explanation for the course of the reaction is quite
3.3 Investigating the

w
straightforward. When the enzyme and substrate are

ie
id
first mixed, there are a large number of substrate

ev
br
progress of an enzyme- am molecules. At any moment, almost every enzyme

-R
molecule has a substrate molecule in its active site. The
catalysed reaction rate at which the reaction occurs depends on:
-C

s
• how many enzyme molecules there are

es
Measuring the rate of • the speed at which the enzyme can convert the
y

Pr
op

substrate into product, release it, and then bind

formation of a product with another substrate molecule.

ity
C

You may be able to carry out an investigation into the However, as more and more substrate is converted into

rs
w

progress of an enzyme-controlled reaction by measuring product, there are fewer and fewer substrate molecules
ie

ve
the rate at which the product is formed from the to bind with enzymes. Enzyme molecules may be

y
ev

substrate. ‘waiting’ for substrate molecules to hit their active sites.

op
ni

As fewer and fewer substrate molecules are left, the

R

Figure 3.6 shows the results of such an investigation

C
reaction gets slower and slower, until it eventually stops.
using the enzyme catalase. This enzyme is found in
ge

w
the tissues of most living things and catalyses the The curve of a graph such as the one in Figure 3.6 is

ie
id

breakdown of hydrogen peroxide into water and oxygen. therefore steepest at the beginning of the reaction: the

ev
br

(Hydrogen peroxide is sometimes produced inside cells. rate of an enzyme-controlled reaction is always fastest
at the beginning. This rate is called the initial rate of
am

It is toxic (poisonous), so it must be got rid of quickly.)

-R
The oxygen that is released can be collected and reaction. You can measure the initial rate of the reaction
by calculating the slope of a tangent to the curve, as
-C

measured, so it is an easy reaction to follow.

s

close to time 0 as possible (see Figure P1.9 for advice

es

9 on how to do this). An easier way of doing it is simply

y
Total volume O2 collected / cm3

Pr
op

to read off the graph the amount of oxygen given off

8
in the first 30 seconds. In this case, the rate of oxygen
ity
C

7 production in the first 30 seconds is 2.7 cm3 of oxygen

rs

per 30 seconds, or 5.4 cm3 per minute.

w

6
ie

ve

5
Question
y
ev

4
op
ni

2 Why is it better to calculate the initial rate of

R

3
C

reaction from a curve such as the one in Figure 3.6

2
ge

than simply by measuring how much oxygen is

w

1 given off in 30 seconds?

ie
id

0
ev
br

0 30 60 90 120 150 180 210 240 270 300 330 360 390
Using a colorimeter to
am

-R

Time / s
measure the progress of an
-C

Figure 3.6: The course of an enzyme-catalysed reaction.

s

Catalase was added to hydrogen peroxide at time 0. The enzyme-controlled reaction

es

gas released was collected in a gas syringe, the volume

y

Pr

If the method used for measuring the progress of an

op

being read at 30 s intervals.

enzyme-controlled reaction involves a colour change, a
ity
C

colorimeter can be used to measure the colour change

The reaction begins very quickly. As soon as the enzyme
rs
w

and substrate are mixed, bubbles of oxygen are released.

KEY WORD
ie

ve

A large volume of oxygen is collected in the first minute

y
ev

of the reaction. As the reaction continues, however, the

op
ni

colorimeter: an instrument that measures the

rate at which oxygen is released gradually slows down.
R

colour of a solution by measuring the absorption

C

The reaction gets slower and slower, until it eventually of different wavelengths of light
e

stops completely.
w
g

ie
id

ev
br
am

-R

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ni
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ge

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PRACTICAL ACTIVITY 3.1

ie
id

ev
br
Measuring the rate of disappearance of a in the reaction mixture decreases. The colour of the
substrateam samples tested will, therefore, change from blue-

-R
black to brown to pale brown and finally remain
Sometimes it is easier to measure the rate of
colourless. You can time how long it takes for the
-C

disappearance of a substrate than the rate of

s
starch to disappear completely, that is, how long

es
appearance of a product. A good example of this
before the iodine test gives a colourless result.
y

is using the enzyme amylase. Amylase breaks down

Pr
Alternatively, a suitable end-point can be chosen,
op

starch to the reducing sugar maltose, a hydrolysis

such as the time taken to reach a pale brown colour
reaction. Starch reacts with iodine solution to

ity
C

in the iodine test.

produce a blue-black colour. During the reaction,

rs
w

small samples can be taken at known times to test (See Practical Investigation 3.3 in the Practical
ie

ve
for starch using iodine solution. As the starch is Workbook for additional information.)

y
ev

converted to maltose, the concentration of starch

op
ni
R

C
quantitatively. This will provide numbers that can be
ge

If you do this over a period of time, you can plot a curve

w
plotted on a graph. A colorimeter is an instrument that of ‘amount of starch remaining’ against ‘time’. You can

ie
id

measures the colour of a solution by measuring the then calculate the initial reaction rate in the same way

ev
br

absorption of different wavelengths of light. The greater as for the catalase/hydrogen peroxide reaction described
am

the absorption, the greater the concentration of the previously.

-R
substance causing the colour. Figure 3.7a shows the main
It is even easier to observe the course of this reaction if
-C

components of a colorimeter.
s

you mix starch, iodine solution and amylase in a tube,

es

In the amylase/starch experiment described in Practical and take regular readings of the colour of the mixture
y

Activity 3.1 you can measure the intensity of the in this one tube in a colorimeter. However, this is not
Pr
op

blue-black colour obtained in the iodine test using a ideal, because the iodine interferes with the rate of the
ity
C

colorimeter. The colour acts as a measure of the amount reaction and slows it down.
of starch still remaining. Figure 3.7b shows a typical
rs
w

range of colours.
ie

ve

y
a
ev

op
ni
R

C
ge

w
ie
id

ev
br
am

-R

solution in a light meter

tube or ‘cuvette’ and readout
-C

light filter
s
es

b
y

Pr
op

ity
C

rs
w
ie

ve

y
ev

op
ni
R

Figure 3.7: a Diagram showing how a colorimeter works. b Photograph of a range of colours obtained with the iodine test
C

during the course of an experiment investigating the digestion of starch by amylase. The tubes show increasing time for
e

w
g

digestion of the starch from left to right.

ie
id

ev
br
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-R

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3 Enzymes

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Question However, above a certain temperature, the enzyme

w
molecule vibrates so much that some of the bonds

ie
id
3 a In the breakdown of starch by amylase, if you holding the enzyme molecule in its precise shape begin

ev
br
were to plot the amount of starch remaining
am to break. This is especially true for hydrogen bonds.

-R
against time, draw the curve you would expect The enzyme’s active site begins to lose its shape and
to obtain. therefore its activity: it is said to be denatured. At first,
-C

b the substrate molecule fits less well into the active site

s
How could you use this curve to calculate the

es
initial reaction rate? of the enzyme, so the rate of the reaction begins to slow
y

down. Eventually the substrate no longer fits at all and

Pr
op

the reaction stops (the rate becomes zero).

3.4 Factors that affect

ity
C

The temperature at which an enzyme catalyses a reaction

at the maximum rate is called the optimum temperature.

rs
w

enzyme action Most human enzymes have an optimum temperature

ie

ve
of around 40 °C. By keeping our body temperatures at

y
ev

op
ni
about 37 °C, we ensure that enzyme-catalysed reactions
The effect of temperature on
R

occur at close to their maximum rate.

U

C
the rate of enzyme activity Enzymes from other organisms may have different
ge

w
optimum temperatures. Some enzymes, such as those found

ie
id

Figure 3.8 shows the effect of temperature on the rate in bacteria which live in hot springs (Figure 3.9), have much

ev
of activity of a typical enzyme. At low temperatures,
br

higher optimum temperatures. Some plant enzymes have

the reaction takes place only very slowly. This is because lower optimum temperatures, depending on their habitat.
am

-R
molecules are moving relatively slowly. In other words,
their kinetic energy is relatively low. Substrate molecules
-C

will not often collide with the active site of the enzyme.
es

As temperature rises, the kinetic energy of the molecules

y

Pr

increases and so the enzyme and substrate molecules

op

move faster. Collisions happen more frequently, so that

ity
C

substrate molecules enter the active site more often. Also,

when substrate and enzyme molecules collide, they do so
rs
w

with more energy. This makes it easier for bonds to be

ie

ve

formed or broken so that the reaction can occur.

y
ev

op
ni
R

enzyme
becoming
ge

denatured
Rate of reaction

ie
id

ev
br
am

-R

Figure 3.9: Not all enzymes have an optimum temperature

optimum of 40 °C. Bacteria and algae living in hot springs such as this
-C

temperature one in Yellowstone National Park, USA, are able to tolerate

s
es

very high temperatures. Enzymes from such organisms are

enzyme
useful in various commercial applications, such as biological
y

completely
Pr
op

denatured washing powders.

0 10 20 30 40 50 60
ity
C

Temperature / °C
rs
w

The effect of pH on the rate of

ie

ve

Figure 3.8: The effect of temperature on the rate of an

y

enzyme-controlled reaction.
ev

enzyme activity
op
ni
R

As temperature continues to increase, kinetic energy Figure 3.10 shows the effect of pH on the rate of
C

increases so the speed of movement of the substrate activity of a typical enzyme. Most enzymes work fastest
e

w
g

and enzyme molecules also continues to increase. at a pH of somewhere around 7, that is, in fairly neutral
ie
id

ev
br
am

-R

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ni
U

C
ge
conditions. Some, however, have a different optimum 5 Proteases are used in biological washing powders.

w
pH. For example, pepsin, an enzyme found in the acidic a How does a protease remove a blood stain

ie
id
conditions of the stomach, has an optimum pH of from clothes?

ev
br
about 1.5. Pepsin is a protease, an enzyme that catalyses
am b Most biological washing powders are

-R
the digestion of proteins.
recommended for use at low washing
temperatures. Why is this?
-C

s
c Washing powder manufacturers have produced

es
proteases which can work at temperatures
y

Pr
Rate of reaction
op

higher than 40 °C. Why is this useful?

6 Trypsin is a protease secreted in pancreatic juice,

ity
C

which acts in the duodenum. If you add trypsin

rs
w

optimum pH to a suspension of milk powder in water, the

ie

ve
enzyme digests the protein in the milk, so that the

y
ev

suspension becomes clear.

op
ni

How could you carry out an investigation into the

R

C
1 3 5 7 9 11 13 effect of pH on the rate of activity of trypsin?
ge

(A suspension of 4 g of milk powder in 100 cm3 of

w
pH
water will become clear in a few minutes if an equal

ie
id

Figure 3.10: The effect of pH on the rate of an enzyme- volume of a 0.5% trypsin solution is added to it.)

ev
br

controlled reaction. The optimum pH depends on the

am

enzyme: in this case, the optimum pH is 7.

-R
The effect of enzyme
-C

pH is a measure of the concentration of hydrogen ions concentration on the

es

in a solution. The lower the pH, the higher the hydrogen

y

ion concentration. Hydrogen ions are positively charged, rate of enzyme activity
Pr
op

so they are attracted to negatively charged ions and

Figure 3.11a shows the results of an investigation using
ity
C

repelled by positively charged ions. Hydrogen ions can

therefore interact with any charged R groups on the the enzyme catalase and its substrate hydrogen peroxide.
rs
w

amino acids of enzyme molecules. This may break the The catalase is present in an extract made from celery.
ie

ve

ionic bonding between the R groups (Chapter 2), which Different concentrations of catalase solution were
y
ev

added to hydrogen peroxide solutions. The different

op
ni

affects the three-dimensional structure of the enzyme

molecule. The shape of the active site may change and concentrations were prepared by varying the initial
R

therefore reduce the chances of the substrate molecule volume of celery extract and then making up to a
ge

standard volume with distilled water. The quantity of

w

fitting into it. A pH which is different from the optimum

hydrogen peroxide (substrate) used was the same at the
ie

pH can cause denaturation of an enzyme.

id

start of all five reactions.

ev
br

When investigating pH, you can use buffer solutions

You can see that the shape of all five curves is similar
am

(Chapter P1, Section P1.3, Variables and making

-R

measurements). Buffer solutions each have a particular (Figure 3.11a). In each case, the reaction begins very
quickly (a steep curve) and then gradually slows down
-C

pH and maintain that pH even if the reaction taking

s

place would otherwise cause the pH to change. You (the curve levels off).
es

add a measured volume of the buffer to your reaction

y

In order to look at the effect of enzyme concentration

Pr
op

mixture. on reaction rate, you must compare the rates of these

five reactions. It is best to look at the rate right at
ity
C

the beginning of the reaction. This is because, once

Questions
rs
w

the reaction is under way, the amount of substrate

ie

ve

4 How could you carry out an experiment to in each reaction begins to vary, because substrate is
y
ev

converted to product at different rates in each of the

op
ni

determine the effect of temperature on the rate of

five reactions. It is only at the very beginning that you
R

breakdown of hydrogen peroxide by catalase?

U

can be sure that the substrate concentration is the same

e

w
g

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id

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-R

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3 Enzymes

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initial volume of extract

w
a 10 4.0 cm3

ie
id
9 3.0 cm3
Total volume O2 collected / cm3

ev
br

Initial rate of reaction / cm3 O2 min−1

b 8
8 am 3
2.0 cm

-R
7
7
6
-C

s
5
1.0 cm3

es
5
4
y

Pr
op

3
3
0.5 cm3
2

ity
C

2
1
1

rs
w

0
ie

0
ve
0 30 60 90 120 150 180 210 240 0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0

y
ev

Time / s Enzyme concentration / cm3 of celery extract

op
ni
R

C
Figure 3.11: The effect of enzyme concentration on the rate of an enzyme-catalysed reaction. a Different volumes of celery
ge

extract, which contains catalase, were added to the same volume of hydrogen peroxide. Water was added to make the total

w
volume of the mixture the same in each case. b The rate of reaction in the first 30 s was calculated for each enzyme concentration.

ie
id

ev
br

in each tube. By calculating the initial rates you can be volume of catalase was kept constant. As in the previous
am

-R
sure that differences in reaction rate are caused only experiment, curves of oxygen released against time
by differences in enzyme concentration and not by were plotted for each reaction, and the initial rate of
-C

substrate concentration. reaction calculated for the first 30 seconds. These initial
es

rates of reaction were then plotted against substrate

To work out the initial rate for each enzyme
y

concentration.
Pr
op

concentration, you can calculate the slope of the curve

30 seconds after the beginning of the reaction, as
ity
C

explained in Chapter P1 (Section P1.3, Variables and Vmax

rs
w

making measurements). Ideally, you should do this for

ie

an even earlier stage of the reaction, but in practice

Initial rate of reaction
ve

y
this is impossible. You can then plot a second graph,
ev

op
ni

Figure 3.11b, showing the initial rate of reaction against

R

enzyme concentration.
C
ge

This graph shows that the initial rate of reaction

w

increases linearly. In these conditions, reaction rate

ie
id

is directly proportional to the enzyme concentration.

ev
br

This is just what common sense says should happen.

am

-R

The more enzyme present, the more active sites will be

available for the substrate to slot into. As long as there
-C

Substrate concentration
s

is plenty of substrate available, the initial rate of a

es

reaction increases linearly with enzyme concentration. Figure 3.12: The effect of substrate concentration on the
y

rate of an enzyme-catalysed reaction.

Pr
op

The effect of substrate

ity
C

As substrate concentration increases, the initial rate of

reaction also increases. This is what you would expect:
concentration on the rate of
rs
w

the more substrate molecules there are, the more often

ie

ve

one will enter an active site. However, if you go on

enzyme activity
y
ev

op
ni

increasing substrate concentration, keeping the enzyme

R

concentration constant, there comes a point when every

U

Figure 3.12 shows the results of an investigation using

C

the enzyme catalase and its substrate hydrogen peroxide. enzyme active site is full. If more substrate is added, the
e

The volume of hydrogen peroxide was varied and the enzyme simply cannot work faster; substrate molecules
g

ie
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am

-R

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ni
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are effectively ‘queuing up’ for an active site to become At Vmax all the enzyme molecules are bound to substrate

w
vacant. The enzyme is working at its maximum possible molecules – the enzyme is saturated with substrate. All

ie
id
rate, known as Vmax. V stands for velocity (speed), max the active sites are full. Vmax can be measured in the way

ev
br
stands for maximum.
am described in Figure 3.11b. The initial rate of the reaction

-R
is measured at different substrate concentrations
KEY WORD while keeping the enzyme concentration constant. As
-C

substrate concentration is increased, reaction rate rises

s
es
Vmax: the theoretical maximum rate of an enzyme- until the reaction reaches its maximum rate, Vmax.
controlled reaction, obtained when all the active
y

Pr
op

sites of the enzyme are occupied

Question

ity
C

8 For each substrate concentration tested, the

rs
w

rate should be measured as soon as possible.

Question
ie

ve
Explain why.

y
ev

op
ni
7 Sketch the shape that the graph in Figure 3.11b The initial rate for each substrate concentration is plotted
R

would have if excess hydrogen peroxide were not

C
against substrate concentration, producing a curve like
available.
ge

those shown in Figures 3.12 and 3.13. Unfortunately, this

w
type of curve never completely flattens out in practice,

ie
id

as shown by the dashed line on both figures. It only

3.5 Comparing enzyme
ev
br

does so in theory at infinite substrate concentration.

am

-R You cannot, therefore, read off the value of Vmax from

affinities the graphs in Figure 3.12 and 3.13. (Note that Vmax is
-C

at the end of the dashed line in the figures.) There is a

s

Affinity is a measure of the strength of attraction

es

mathematical way out of this problem. From the data

between two things. A high affinity means there is a
y

in such graphs, it is possible to calculate ½Vmax. You do

Pr
op

strong attraction. When applied to enzymes, affinity not need to understand how to do this. ½Vmax is exactly
is a measure of the strength of attraction between the half the maximum velocity. It is just as useful as Vmax
ity
C

enzyme and its substrate. The greater the affinity of an as an indicator of how fast an enzyme works. You can
rs
w

enzyme for its substrate, the faster it works. Another plot ½Vmax on a graph like Figures 3.12 and 3.13, and
ie

way of thinking about this is to say that the higher the

ve

from that find the substrate concentration that will result

y
affinity, the more likely it is that the product will be
ev

in ½Vmax. This is the substrate concentration at which

op
ni

formed when a substrate molecule enters the active site. half the enzyme’s active sites are occupied by substrate.
R

If the affinity is low, the substrate may leave the active

C

Figure 3.13 shows a graph with ½Vmax added. You will

site before a reaction takes place.
ge

There is enormous variation in the speed at which

ie
id

Vmax
different enzymes work. A typical enzyme molecule can
ev
br

convert around 1000 substrate molecules into product

am

-R

per second. The enzyme carbonic anhydrase (Chapter 8,

Section 8.5, Blood) is one of the fastest enzymes known.
-C

It can remove 600 000 molecules of carbon dioxide from 1

V
es

respiring tissue per second. This is roughly 107 times as 2 max

y

fast as the reaction would occur without the enzyme. It

Pr

Initial rate
op

has presumably evolved such a high efficiency because

ity

a build-up of carbon dioxide in tissues would become

C

lethal very quickly.

rs
w
ie

In the previous section, you saw that a useful indicator

ve

Km Substrate concentration
y

of the efficiency of an enzyme is its Vmax. This tells

ev

op
ni

you the maximum speed at which an enzyme works. Figure 3.13: A graph showing the effect of substrate
R

Remember, V stands for velocity, which means speed. concentration on initial rate of an enzyme reaction, with
C

Vmax, ½ Vmax and Km values shown.

e

w
g

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id

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-R

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3 Enzymes

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Enzyme Substrate Vmax / arbitrary units Km / µmol dm–3

ie
id
carbonic anhydrase carbon dioxide 600 000 8000

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penicillinaseam penicillin 2000 50

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chymotrypsin protein 100 5000
-C

lysozyme acetylglucosamine 0.5 6

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Table 3.1: Vmax and Km values for four enzymes. Note that the unit for Km is a concentration.

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see that the substrate concentration which causes ½Vmax b i Which enzyme had the higher Michaelis–

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is labelled Km. Km is known as the Michaelis–Menten Menten constant?

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constant. The Michaelis–Menten constant of an enzyme

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ii Which enzyme had the higher Vmax?

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is the substrate concentration at which the enzyme works
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iii Which enzyme required the greater

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at half its maximum rate. It is used as a measure of the

concentration of substrate to
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affinity of the enzyme for its substrate.

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achieve Vmax?
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iv Which enzyme required the greater
KEY WORD

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concentration of substrate to saturate its

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active sites?
Michaelis–Menten constant (Km): the substrate
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concentration at which an enzyme works at half

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its maximum rate (½Vmax), used as a measure of
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the efficiency of an enzyme; the lower the value

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of Km, the more efficient the enzyme

y

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If you think about it, the higher the affinity of an

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enzyme for its substrate, the lower the substrate

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concentration needed before ½Vmax is reached. The

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lower the substrate concentration, the lower the value

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of Km (see Figure 3.13). So the higher the affinity of an

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enzyme for its substrate, the lower its Km will be.

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Figure 3.14: Comparison of affinity of two different

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enzymes for their substrates.

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Questions
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3.6 Enzyme inhibitors

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9 Which of the four enzymes in Table 3.1:

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a works fastest?
b has the highest affinity for its substrate? Briefly Competitive, reversible
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explain your answer.

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10 Figure 3.14 shows the results of two experiments. inhibition

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The aim of the experiments was to compare

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As you have seen, the active site of an enzyme fits

the affinity of two different enzymes for their its substrate perfectly. It is possible, however, for a
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substrates. Enzyme A had a higher affinity for its molecule which is similar in shape to the substrate to
substrate than enzyme B. The two curves plot the
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enter an enzyme’s active site. This would then inhibit the

results obtained for enzyme A and enzyme B.
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enzyme’s function.
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a Copy Figure 3.14 and:

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If an inhibitor molecule binds only briefly to the site

i label the axes appropriately
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and comes out again, there is competition between it

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ii label appropriately one curve enzyme A and and the substrate for the site. If there is much more
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one curve enzyme B.

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of the substrate present than the inhibitor, substrate

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molecules can easily ‘win’ the competition, and so the damage. However, the active site of the enzyme which

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enzyme’s function is more or less unaffected. However, converts ethylene glycol to oxalic acid will also accept

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if the concentration of the inhibitor rises or that of ethanol. If the poisoned person is given a large dose of

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the substrate falls, it becomes less and less likely that
am ethanol, the ethanol acts as a competitive inhibitor, slowing

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the substrate will collide with an empty active site. The down the action of the enzyme on ethylene glycol for long
enzyme’s function is then inhibited. This is known as enough to allow the ethylene glycol to be excreted.
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competitive inhibition (Figure 3.15a). It is said to be

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reversible (not permanent) because it can be reversed
Non-competitive, reversible
y

by increasing the concentration of the substrate. This is

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how you can tell the difference between competitive and

non-competitive inhibition (Figure 3.15). inhibition

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a Competitive inhibition A different kind of reversible inhibition is possible

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which is non-competitive. In this type of inhibition, the

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substrate fits inhibitor molecule binds to another part of the enzyme,

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precisely into the not the active site. While the inhibitor is bound to the
enzyme’s active site
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enzyme, it can seriously affect the normal arrangement

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active site of hydrogen bonds and hydrophobic interactions
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holding the enzyme molecule in its three-dimensional

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competitive inhibitor
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shape. The resulting distortion changes the shape of

has a similar shape to

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the active site and therefore inhibits the ability of the

the substrate and fits
substrate to enter the active site. While the inhibitor
am

into the enzyme’s

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active site is attached to the enzyme, the enzyme’s function is
blocked. The substrate molecule and the inhibitor are
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not competing for the active site, so this is an example of

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non-competitive inhibition (Figure 3.15b). Increasing the

y

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substrate concentration has no effect on the inhibition,

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enzyme unlike the case with competitive inhibition.

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Inhibition of an enzyme can be harmful or even fatal

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b Non-competitive inhibition but, in many situations, inhibition is essential. For

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active site example, metabolic reactions must be controlled so that

Other molecules may bind
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no enzyme can be allowed to work without stopping at

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elsewhere on the enzyme,

some point, otherwise more and more product would
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changing the shape of its

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active site. constantly be being made.

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KEY WORDS
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competitive inhibition: when a substance

am

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non-competitive inhibitor reduces the rate of activity of an enzyme by

competing with the substrate molecules for
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the enzyme’s active site; increasing substrate

s

enzyme
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concentration reduces the degree of inhibition;

y

Figure 3.15: Enzyme inhibition: a competitive inhibition; increasing inhibitor concentration increases the
Pr
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b non-competitive inhibition. Both these types of inhibition degree of inhibition

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are reversible.
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non-competitive inhibition: when a substance

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reduces the rate of activity of an enzyme, but

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An example of competitive inhibition occurs in the increasing the concentration of the substrate
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treatment of a person who has drunk ethylene glycol.

y

does not reduce the degree of inhibition; many

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Ethylene glycol is used as antifreeze, and is sometimes non-competitive inhibitors bind to areas of the
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drunk accidentally. Ethylene glycol is rapidly converted in enzyme molecule other than the active site itself
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the body to oxalic acid, which can cause irreversible kidney

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3 Enzymes

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One way of controlling metabolic reactions is to use The enzyme lactase can be immobilised using alginate

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the end product of a chain of reactions as a non- beads (Figure 3.17 in Practical Activity 3.2). The

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competitive, reversible inhibitor (Figure 3.16). The substrate of lactase is the disaccharide sugar lactose.

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end product inhibits the enzyme at the beginning
am Milk is allowed to run through a column of lactase-

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of the chain of reactions (enzyme 1 in Figure 3.16). containing beads (Figure 3.18). The lactase hydrolyses
The enzyme is gradually slowed down as the amount the lactose in the milk to glucose and galactose. The
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of end product increases. However, the end product milk is therefore lactose-free, and can be used to make

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can lose its attachment to the enzyme (the reaction is lactose-free dairy products for people who cannot digest
y

reversible) so, if it gets used somewhere else, the enzyme lactose.

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returns to its active state and makes more end product.

You can see that enzyme immobilisation has several
This way of regulating the amount of end product

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obvious advantages compared with just mixing up the

formed is called end product inhibition.
enzyme with its substrate. If you just mixed lactase

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inhibition with milk, you would have a very difficult job to get the
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lactase back again. Not only would you lose the lactase,

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enzyme 1 enzyme 2 enzyme 3 but you would also have milk contaminated with the
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enzyme. Using immobilised enzymes means that you

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can keep and re-use the enzymes, and that the product is
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enzyme-free.

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substrate product 1 product 2 product 3

(end product) Another advantage of this process is that the immobilised

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enzymes are more tolerant of temperature changes and

am

Figure 3.16: End product inhibition. As levels of product

-R
pH changes than enzymes in solution. This may be partly
3 rise, there is increasing inhibition of enzyme 1. So, less because their molecules are held firmly in shape by the
-C

product 1 is made and therefore less product 2 and 3. alginate in which they are embedded, and so do not
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Falling levels of product 3 allow increased function of denature so easily. It may also be because the parts of the
y

enzyme 1 so products 1, 2 and 3 rise again and the cycle molecules that are embedded in the beads are not fully
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continues. This end product inhibition finely controls exposed to the temperature or pH changes.
levels of product 3 between narrow upper and lower
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limits, and is an example of a feedback mechanism.

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Questions
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11 a
y
Outline an investigation you could carry out
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to compare the temperature at which the

3.7 Immobilising
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enzyme lactase is completely denatured within

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ten minutes
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enzymes i when free in solution

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ii when immobilised in alginate beads.

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Enzymes have an enormous range of commercial

applications – for example, in medicine, food technology b Outline an experiment you could carry out to
am

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and industrial processes. Enzymes are expensive. No investigate how long it takes the enzyme lactase
company wants to have to keep buying them over and to denature at 90 °C
-C

over again if it can recycle them in some way. One of the i when free in solution
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best ways of keeping costs down is to use immobilised ii when immobilised in alginate beads.
y

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enzymes. Immobilised enzymes are fixed in some way to

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c Outline how you would determine the optimum

prevent them from diffusing freely in a solution.
pH of the enzyme lactase
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i when free in solution

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KEY WORD
ii when immobilised in alginate beads.
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immobilised enzymes: enzymes that have been

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12 Summarise the advantages of using immobilised

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fixed to a surface or trapped inside beads of enzymes rather than enzyme solutions.
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agar gel
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PRACTICAL ACTIVITY 3.2

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Immobilising enzymes
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mixture of sodium alginate solution and lactase
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milk
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When small drops of the
C

mixture enter calcium

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chloride solution, they alginate beads containing

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immobilised lactase
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form ‘beads’. The alginate

y
holds the enzyme
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molecules in the beads.

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Figure 3.17: Immobilising enzyme in alginate.
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Figure 3.17 shows one way in which enzymes can be
id

immobilised. The enzyme is mixed with a solution milk free of lactose

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and lactase
of sodium alginate. Little droplets of this mixture
am

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are then added to a solution of calcium chloride.
The sodium alginate and calcium chloride instantly
-C

react to form jelly, which turns each droplet into a

es

little bead. The jelly bead contains the enzyme. The

y

enzyme is held in the bead, or immobilised.

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Figure 3.18: Using immobilised enzyme to modify milk.

These beads can be packed gently into a column.
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A liquid containing the enzyme’s substrate can be

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allowed to trickle steadily over them (Figure 3.18). (See Practical Investigation 3.5 in the Practical
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Workbook for additional information.)

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As the substrate runs over the surface of the beads,
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the enzymes in the beads catalyse a reaction that

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converts the substrate into product. The product

C

continues to trickle down the column, emerging

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from the bottom, where it can be collected and

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purified.
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REFLECTION
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If you were designing a new enzyme to solve a Final reflection

es

complex biological or chemical problem, what

y

Discuss with a friend which, if any, parts of

Pr
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characteristics and features would it be useful to be Chapter 3 you need to:

able to control? Try to think of both structural and
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functional features. Can you think of any new uses • read through again to make sure you really
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for enzymes, such as substances it would be useful understand

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to be able to break down using enzymes? • seek more guidance on, even after going over
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Personal reflection question it again.

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If you were the teacher, what comments would you

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make about your performance in this activity?

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3 Enzymes

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SUMMARY

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Enzymes are globular proteins which catalyse metabolic reactions. Each enzyme has an active site with a flexible
structure which can change shape slightly to fit precisely the substrate molecule. This is called the induced-fit
am

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hypothesis.
-C

s
Enzymes may be involved in reactions which break down molecules or join molecules together. They work by

es
lowering the activation energy of the reactions they catalyse.
y

Pr
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The course of an enzyme reaction can be followed by measuring the rate at which a product is formed or the
rate at which a substrate disappears. A progress curve, with time on the x-axis, can be plotted. The curve is

ity
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steepest at the beginning of the reaction, when substrate concentration is at its highest. This rate is called the

rs
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initial rate of reaction.

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Temperature, pH, enzyme concentration and substrate concentration all affect the rate of activity of enzymes.

y
ev

op
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Each enzyme has an optimum temperature at which it works fastest. As temperature increases above the
R

C
optimum temperature, the enzyme gradually denatures (loses its precise tertiary structure).
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Each enzyme has an optimum pH. Some enzymes operate within a narrow pH range; some have a broad pH range.

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id

The greater the concentration of the enzyme, the faster the rate of reaction, provided there are enough substrate

ev
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molecules present. The greater the concentration of the substrate, the faster the rate of reaction, provided enough
am

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enzyme molecules are present. During enzyme reactions, rates slow down as substrate molecules are used up.
The efficiency of an enzyme can be measured by finding the value known as the Michaelis–Menten constant, Km.
-C

To do this, the maximum rate of reaction, Vmax, must first be determined. Determination of Vmax involves finding
es

the initial rates of reactions at different substrate concentrations while ensuring that enzyme concentration
y

Pr

remains constant.
op

Enzymes are affected by the presence of inhibitors, which slow down or stop their activity. Competitive inhibitors
ity
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have a similar shape to the normal substrate molecules. They compete with the substrate for the active site of the
rs
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enzyme. Competitive inhibition is reversible because the inhibitor can enter and leave the active site.
ie

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y
Reversible non-competitive inhibitors bind at a site elsewhere on the enzyme, causing a change in shape of the
ev

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active site.
R

Enzymes can be immobilised – for example, by trapping them in jelly (alginate) beads. This is commercially
ge

useful because the enzyme can be re-used and the product is separate from (uncontaminated by) the enzyme.
w

Immobilisation often makes enzymes more stable.

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am

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