Cambridge International AS and A Level Biology Coursebook

Mary Jones, Richard Fosbery,
Jennifer Gregory and Dennis Taylor

Cambridge International AS and A Level

Biology

Coursebook

Fourth Edition



Mary Jones, Richard Fosbery,
Jennifer Gregory and Dennis Taylor

Cambridge International AS and A Level

Biology
Coursebook

Fourth Edition

University Printing House, Cambridge cb2 8bs, United Kingdom
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First published 2003
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Contents

How to use this book vi 5 The mitotic cell cycle 93

Introduction viii Chromosomes 94

Mitosis 97

1 Cell structure 1 The significance of telomeres 102

Why cells? 3 Stem cells 103

Cell biology and microscopy 3 Cancer 103

Animal and plant cells have features in common 5 End-of-chapter questions 106

Differences between animal and plant cells 5 6 Nucleic acids and protein synthesis 110

Units of measurement in cell studies 6 The structure of DNA and RNA 111
DNA replication 113
Electron microscopy 6 Genes and mutations 118
DNA, RNA and protein synthesis 118
Ultrastructure of an animal cell 13 End-of-chapter questions 123

Ultrastructure of a plant cell 19

Two fundamentally different types of cell 21

End-of-chapter questions 23

2 Biological molecules 27 7 Transport in plants 126

The building blocks of life 28 The transport needs of plants 127

Monomers, polymers and macromolecules 29 Two systems: xylem and phloem 128

Carbohydrates 29 Structure of stems, roots and leaves 128

Lipids 36 The transport of water 134 iii

Proteins 39 Transport of mineral ions 146

Water 46 Translocation 146

End-of-chapter questions 49 Differences between sieve tubes and

xylem vessels 151

3 Enzymes 53 End-of-chapter questions 153

Mode of action of enzymes 54 8 Transport in mammals 157
Factors that affect enzyme action 57
Enzyme inhibitors 61 Transport systems in animals 158
Comparing the affinity of different enzymes for
62 The mammalian cardiovascular system 158
their substrates 64
Immobilising enzymes 66 Blood vessels 160
End-of-chapter questions
Blood plasma and tissue fluid 164

Lymph 164

Blood 166

4 Cell membranes and transport 72 Haemoglobin 168

Phospholipids 73 Problems with oxygen transport 171

Structure of membranes 74 The heart 173

Cell signalling 77 The cardiac cycle 175

Movement of substances into and out of cells 79 Control of the heart beat 177

End-of-chapter questions 89 End-of-chapter questions 179

Cambridge International AS LaenvdeAl BLieovleolgByiology

9 Gas exchange and smoking 185 12 Energy and respiration 267

Gas exchange 186 The need for energy in living organisms 268

Lungs 186 Work 269

Trachea, bronchi and bronchioles 187 ATP 270

Alveoli 189 Respiration 272

Smoking 190 Mitochondrial structure and function 276

Tobacco smoke 190 Respiration without oxygen 277

Lung diseases 190 Respiratory substrates 278

Short-term effects on the cardiovascular system 193 Adaptations of rice for wet environments 281

End-of-chapter questions 195 End-of-chapter questions 283

10 Infectious diseases 198 13 Photosynthesis 286

Worldwide importance of infectious diseases 200 An energy transfer process 287

Cholera 200 The light dependent reactions of photosynthesis 288

Malaria 202 The light independent reactions of

Acquired immune deficiency syndrome (AIDS) 205 photosynthesis 290

Tuberculosis (TB) 209 Chloroplast structure and function 290

Measles 212 Factors necessary for photosynthesis 291

Antibiotics 213 C4 plants 293

End-of-chapter questions 219 Trapping light energy 295

11 Immunity 222 End-of-chapter questions 297

Defence against disease 223 14 Homeostasis 299
224
iv Cells of the immune system 232 Internal environment 300
Active and passive immunity
237 Control of homeostatic mechanisms 301
242
Autoimmune diseases – a case of The control of body temperature 302

mistaken identity Excretion 304

End-of-chapter questions The structure of the kidney 305

P1 Practical skills for AS 246 Control of water content 312

The control of blood glucose 315

Experiments 247 Urine analysis 319

Variables and making measurements 247 Homeostasis in plants 320

Estimating uncertainty in measurement 255 End-of-chapter questions 325

Recording quantitative results 255 15 Coordination 329

Constructing a line graph 256 Nervous communication 330
Muscle contraction 344
Constructing bar charts and histograms 258 Hormonal communication 349
Birth control 351
Making conclusions 259 Control and coordination in plants 353
End-of-chapter questions 358
Describing data 259

Making calculations from data 259

Explaining your results 261

Identifying sources of error and suggesting

improvements 261

Drawings 262

End-of-chapter questions 264

Contents

16 Inherited change 364 19 Genetic technology 462 v

Homologous chromosomes 365 Genetic engineering 463
Two types of nuclear division 367 Tools for the gene technologist 464
M iosis 368 Genetic technology and medicine 475
G n tics 374 Gene therapy 477
Genotype affects phenotype 374 Genetic technology and agriculture 480
Inheriting genes 375 End-of-chapter questions 487
Multiple alleles 378
Sex inheritance 378 P2 Planning, analysis and evaluation 490
Sex linkage 379
Dihybrid crosses 380 Planning an investigation 491
Interactions between loci 382 Constructing a hypothesis 491
Autosomal linkage 383 Using the right apparatus 491
Crossing over 384 Identifying variables 492
The χ2 (chi-squared) test 386 Describing the sequence of steps 495
Mutations 387 Risk assessment 495
Gene control in prokaryotes 389 Recording and displaying results 495
Gene control in eukaryotes 391 Analysis, conclusions and evaluation 495
End-of-chapter questions 393 Pearson’s linear correlation 501
Spearman’s rank correlation 503
17 Selection and evolution 397 Evaluating evidence 504
Conclusions and discussion 506
Variation 398 End-of-chapter questions 507
Natural selection 402
Evolution 404 Appendix 1: Amino acid R groups 512
Artificial selection 409
The Darwin–Wallace theory of evolution by Appendix 2: DNA and RNA triplet codes 513
412
natural selection 413 Glossary 514
Species and speciation 416
Molecular comparisons between species 417 Index 526
Extinctions 420
End-of-chapter questions Acknowledgements 534
423
18 Biodiversity, classification and CD-ROM CD1
conservation 425
426 Advice on how to revise for and approach CD1
Ecosyst ms 430 examinations
Biodiv rsity 431 Introduction to the examination and changes CD16
Simpson’s Index of Diversity 433 to the syllabus CD21
Systematic sampling 435 Answers to self-assessment questions CD64
Corr lation 440 Answers to end-of-chapter questions CD128
Classification 441 Recommended resources
Virus s 444
Threats to biodiversity 445
Why does biodiversity matter? 451
Protecting endangered species 452
Controlling alien species 453
International conservation organisations 455
Restoring degraded habitats
End-of-chapter questions

Cambridge International AS Level Biology

How to use this book

Each chapter begins with a short There is a short
list of the facts and concepts that context at the
are explained in it. beginning of each
chapter, containing
an example of how
the material covered
in the chapter relates
to the ʻreal worldʼ.

Questions throughout the text give you a chance to check that you have understood
the topic you have just read about. You can find the answers to these questions on
the CD-ROM.

This book does not contain detailed
instructions for doing particular
experiments, but you will find
background information about
the practical work you need to do
vi in these boxes. There are also two

chapters, P1 and P2, which provide
detailed information about the
practical skills you need to develop
during your course.

The text and illustrations describe and
explain all of the facts and concepts
that you need to know. The chapters,
and often the content within them
as well, are arranged in the same
sequence as in your syllabus.

Important equations and
other facts are shown in
highlight boxes.

Wherever you need to know how to use a formula to carry out a calculation, How to use this book
there are worked example boxes to show you how to do this.
Definitions that are required by the
syllabus are shown in highlight boxes.

Key words are highlighted in the text vii
when they are first introduced.

You will also find definitions of
these words in the Glossary.

There is a summary of key
points at the end of each
chapter. You might find
this helpful when you are
revising.
Questions at the end of each chapter begin with a few multiple choice questions, then move on
to questions that will help you to organise and practise what you have learnt in that chapter.
Finally, there are several more demanding exam-style questions, some of which may require use of
knowledge from previous chapters. Answers to these questions can be found on the CD–ROM.

Cambridge International AS Level Biology

Introduction

This fourth edition of Cambridge International AS and the AS examination you might be asked a question that
A Level Biology provides everything that you need to involves bringing together knowledge about protein
do well in your Cambridge International Examinations synthesis, infectious disease and transport in mammals.
AS and A level Biology (9700) courses. It provides full In particular, you will find that certain key concepts come
coverage of the syllabus for examinations from 2016 up again and again. These include:
onwards.
The chapters are arranged in the same sequence as the ■■ cells as units of life
■■ biochemical processes
material in your syllabus. Chapters 1 to P1 cover the AS ■■ DNA, the molecule of heredity
material, and Chapters 12 to P2 cover the extra material ■■ natural selection
you need for the full A level examinations. The various ■■ organisms in their environment
features that you will find in these chapters are explained
on the next two pages. ■■ observation and experiment

viii In your examinations, you will be asked many As you work through your course, make sure that you
questions that test deep understanding of the facts and keep on thinking about the work that you did earlier, and
concepts that you will learn during your course. It’s how it relates to the current topic that you are studying.
therefore not enough just to learn words and diagrams that On the CD-ROM, you will also find some suggestions
you can repeat in the examination; you need to ensure that for other sources of particularly interesting or useful
you really understand each concept fully. Trying to answer information about the material covered in each chapter.
the questions that you will find within each chapter, and Do try to track down and read some of these.
at the end, should help you to do this. There are answers
to all of these questions on the CD-ROM that comes with Practical skills are an important part of your biology
this book. course. You will develop these skills as you do experiments
and other practical work related to the topic you are
Although you will study your biology as a series of studying. Chapters P1 (for AS) and P2 (for A level) explain
different topics, it’s very important to appreciate that all of what these skills are, and what you need to be able to do to
these topics link up with each other. Some of the questions succeed in the examination papers that test these skills.
in your examination will test your ability to make links
between different areas of the syllabus. For example, in

Chapter 1: Cell structure

Chapter 1: 11
Cell structure

Learning outcomes ■■ discuss the variety of cell structures and their
functions
You should be able to:
■■ describe the organisation of cells into tissues
■■ describe and compare the structure of animal, and organs
plant and bacterial cells, and discuss the non-
cellular nature of viruses ■■ outline the role of ATP in cells

■■ describe the use of light microscopes and
electron microscopes to study cells

■■ draw and measure cell structures

Cambridge International AS Level Biology

Thinking outside the box

Progress in science often depends on people thinking evolutionary change. She continued to challenge the
‘outside the box’ – original thinkers who are often Darwinian view that evolution occurs mainly as a
ignored or even ridiculed when they first put forward result of competition between species.
their radical new ideas. One such individual, who
battled constantly throughout her career to get her
ideas accepted, was the American biologist Lynn
Margulis (born 1938, died 2011: Figure 1.1). Her
greatest achievement was to use evidence from
microbiology to help firmly establish an idea that had
been around since the mid-19th century – that new
organisms can be created from combinations
of existing organisms which are not necessarily
closely related. The organisms form a symbiotic
partnership, typically by one engulfing the other
– a process known as endosymbiosis. Dramatic
evolutionary changes result.
The classic examples, now confirmed by later
work, were the suggestions that mitochondria and
chloroplasts were originally free-living bacteria
(prokaryotes) which invaded the ancestors of modern Figure 1.1  Lynn Margulis: ‘My work more than didn’t fit in.
It crossed the boundaries that people had spent their lives
eukaryotic cells (cells with nuclei). Margulis saw building up. It hits some 30 sub-fields of biology,
such symbiotic unions as a major driving cause of even geology.’

22

In the early days of microscopy an English scientist, Figure 1.2  Drawing of cork cells published by Robert Hooke
Robert Hooke, decided to examine thin slices of plant in 1665.
material. He chose cork as one of his examples. Looking
down the microscope, he was struck by the regular
appearance of the structure, and in 1665 he wrote a book
containing the diagram shown in Figure 1.2.

If you examine the diagram you will see the ‘pore-
like’ regular structures that Hooke called ‘cells’. Each cell
appeared to be an empty box surrounded by a wall. Hooke
had discovered and described, without realising it, the
fundamental unit of all living things.

Although we now know that the cells of cork are dead,
further observations of cells in living materials were
made by Hooke and other scientists. However, it was
not until almost 200 years later that a general cell theory
emerged from the work of two German scientists. In 1838
Schleiden, a botanist, suggested that all plants are made
of cells, and a year later Schwann, a zoologist, suggested
the same for animals. The cell theory states that the basic
unit of structure and function of all living organisms is the
cell. Now, over 170 years later, this idea is one of the most
familiar and important theories in biology. To it has been
added Virchow’s theory of 1855 that all cells arise from
pre-existing cells by cell division.

Chapter 1: Cell structure

Why cells? eyepiece Eyepiece lens magni es
light beam and focuses the image
A cell can be thought of as a bag in which the chemistry from the objective onto
of life is allowed to occur, partially separated from the the eye.
environment outside the cell. The thin membrane which
surrounds all cells is essential in controlling exchange objective Objective lens collects
between the cell and its environment. It is a very effective cover slip light passing through the
barrier, but also allows a controlled traffic of materials glass slide specimen and produces a
across it in both directions. The membrane is therefore magni ed image.
described as partially permeable. If it were freely
permeable, life could not exist, because the chemicals of condenser Condenser lens focuses
the cell would simply mix with the surrounding chemicals iris diaphragm the light onto the
by diffusion. specimen held between
the cover slip and slide.
Cell biology and microscopy
light source Condenser iris
The study of cells has given rise to an important branch of pathway of light diaphragm is closed
biology known as cell biology. Cells can now be studied slightly to produce a
by many different methods, but scientists began simply narrow beam of light.
by looking at them, using various types of microscope.
Figure 1.3 How the light microscope works.
There are two fundamentally different types of
microscope now in use: the light microscope and the 3
electron microscope. Both use a form of radiation in order
to create an image of the specimen being examined. The Golgi body small structures that
light microscope uses light as a source of radiation, while cytoplasm are di cult to identify
the electron microscope uses electrons, for reasons which
are discussed later. mitochondria

Light microscopy cell surface
membrane
The ‘golden age’ of light microscopy could be said to be
the 19th century. Microscopes had been available since centriole – always nuclear envelope nucleus
the beginning of the 17th century but, when dramatic found near nucleus, chromatin –
improvements were made in the quality of glass lenses in has a role in nuclear deeply staining
the early 19th century, interest among scientists became division and thread-like
widespread. The fascination of the microscopic world nucleolus –
that opened up in biology inspired rapid progress both in deeply staining
microscope design and, equally importantly, in preparing
material for examination with microscopes. This branch Figure 1.4 Structure of a generalised animal cell (diameter
of biology is known as cytology. Figure 1.3 shows how the about 20 μm) as seen with a very high quality light microscope.
light microscope works.

By 1900, all the structures shown in Figures 1.4 and
1.5 had been discovered. Figure 1.4 shows the structure of
a generalised animal cell and Figure 1.5 the structure of a
generalised plant cell as seen with a light microscope.
(A generalised cell shows all the structures that are
typically found in a cell.) Figure 1.6 shows some actual
human cells and Figure 1.7 shows an actual plant cell
taken from a leaf.

Cambridge International AS Level Biology

tonoplast – membrane middle lamella – thin layer
surrounding vacuole holding cells together,
contains calcium pectate

cell surface membrane plasmodesma –
(pressed against cell wall) connects cytoplasm
vacuole – large of neighbouring cells
with central position
cytoplasm cell wall of
neighbouring
cell

mitochondria cell wall
chloroplast

nucleus nucleolus – grana just visible
deeply staining
nuclear envelope small structures that
are di cult to identify
chromatin – Golgi apparatus
deeply staining
and thread-like

Figure 1.5  Structure of a generalised plant cell (diameter about 40 μm) as seen with a very high quality light microscope.

4

Figure 1.6  Cells from the lining of the human cheek (× 400), Figure 1.7  Photomicrograph of a cells in a moss leaf (×400).
each showing a centrally placed nucleus, which is a typical
animal cell characteristic. The cells are part of a tissue known
as squamous (flattened) epithelium.

QUESTION
1.1 Using Figures 1.4 and 1.5, name the structures

that animal and plant cells have in common, those
found in only plant cells, and those found only in
animal cells.

Chapter 1: Cell structure

Animal and plant cells Differences between animal 5
have features in common and plant cells

In animals and plants each cell is surrounded by a very The only structure commonly found in animal cells which
thin cell surface membrane. This is also sometimes is absent from plant cells is the centriole. Plant cells also
referred to as the plasma membrane. differ from animal cells in possessing cell walls, large
permanent vacuoles and chloroplasts.
Many of the cell contents are colourless and
transparent so they need to be stained to be seen. Each Centrioles
cell has a nucleus, which is a relatively large structure
that stains intensely and is therefore very conspicuous. Under the light microscope the centriole appears as a small
The deeply staining material in the nucleus is called structure close to the nucleus (Figure 1.4, page 3). Centrioles
chromatin and is a mass of loosely coiled threads. are discussed on page 18.
This material collects together to form visible separate
chromosomes during nuclear division (page 98). It Cell walls and plasmodesmata
contains DNA (deoxyribonucleic acid), a molecule which
contains the instructions that control the activities of the With a light microscope, individual plant cells are more
cell (see Chapter 6). Within the nucleus an even more easily seen than animal cells, because they are usually
deeply staining area is visible, the nucleolus, which is larger and, unlike animal cells, surrounded by a cell wall
made of loops of DNA from several chromosomes. The outside the cell surface membrane. This is relatively rigid
number of nucleoli is variable, one to five being common because it contains fibres of cellulose, a polysaccharide
in mammals. which strengthens the wall. The cell wall gives the cell a
definite shape. It prevents the cell from bursting when
The material between the nucleus and the cell surface water enters by osmosis, allowing large pressures to
membrane is known as cytoplasm. Cytoplasm is an develop inside the cell (page 84). Cell walls may also be
aqueous (watery) material, varying from a fluid to a reinforced with extra cellulose or with a hard material
jelly-like consistency. Many small structures can be seen called lignin for extra strength (page 141). Cell walls are
within it. These have been likened to small organs and freely permeable, allowing free movement of molecules
hence are known as organelles. An organelle can be and ions through to the cell surface membrane.
defined as a functionally and structurally distinct part
of a cell. Organelles themselves are often surrounded Plant cells are linked to neighbouring cells by means of
by membranes so that their activities can be separated fine strands of cytoplasm called plasmodesmata (singular:
from the surrounding cytoplasm. This is described as plasmodesma), which pass through pore-like structures in
compartmentalisation. Having separate compartments their walls. Movement through the pores is thought to be
is essential for a structure as complex as an animal or controlled by the structure of the pores.
plant cell to work efficiently. Since each type of organelle
has its own function, the cell is said to show division of Vacuoles
labour, a sharing of the work between different
specialised organelles. Although animal cells may possess small vacuoles such
as phagocytic vacuoles (page 87), which are temporary
The most numerous organelles seen with the light structures, mature plant cells often possess a large,
microscope are usually mitochondria (singular: permanent, central vacuole. The plant vacuole is
mitochondrion). Mitochondria are only just visible, surrounded by a membrane, the tonoplast, which controls
but films of living cells, taken with the aid of a light exchange between the vacuole and the cytoplasm. The
microscope, have shown that they can move about, fluid in the vacuole is a solution of pigments, enzymes,
change shape and divide. They are specialised to carry sugars and other organic compounds (including some
out aerobic respiration. waste products), mineral salts, oxygen and carbon dioxide.

The use of special stains containing silver enabled the Vacuoles help to regulate the osmotic properties of cells
Golgi apparatus to be detected for the first time in 1898 by (the flow of water inwards and outwards) as well as having
Camillo Golgi. The Golgi apparatus is part of a complex a wide range of other functions. For example, the pigments
internal sorting and distribution system within the cell which colour the petals of certain flowers and parts of
(page 15). It is also sometimes called the Golgi body or some vegetables, such as the red pigment of beetroots, may
Golgi complex. be located in vacuoles.

Cambridge International AS Level Biology

Chloroplasts It is difficult to imagine how small these units are,
but, when looking down a microscope and seeing cells
Chloroplasts are found in the green parts of the plant, clearly, we should not forget how amazingly small the
mainly in the leaves. They are relatively large organelles cells actually are. The smallest structure visible with the
and so are easily seen with a light microscope. It is even human eye is about 50–100 μm in diameter. Your body
possible to see tiny ‘grains’ or grana (singular: granum) contains about 60 million million cells, varying in size
inside the chloroplasts using a light microscope. These from about 5 μm to 40 μm. Try to imagine structures like
are the parts of the chloroplast that contain chlorophyll, mitochondria, which have an average diameter of 1 μm.
the green pigment which absorbs light during the process The smallest cell organelles we deal with in this book,
of photosynthesis, the main function of chloroplasts. ribosomes, are only about 25 nm in diameter! You could
Chloroplasts are discussed further on page 19. line up about 20 000 ribosomes across the full stop at the
end of this sentence.
Points to note
■■ You can think of a plant cell as being very similar to an
animal cell, but with extra structures. Electron microscopy

■■ Plant cells are often larger than animal cells, although As we said on page 3, by 1900 almost all the structures
cell size varies enormously. shown in Figures 1.4 and 1.5 (pages 3 and 4) had been

■■ Do not confuse the cell wall with the cell surface discovered. There followed a time of frustration for
membrane. Cell walls are relatively thick and microscopists, because they realised that no matter how
physically strong, whereas cell surface membranes are much the design of light microscopes improved, there was
very thin. Cell walls are freely permeable, whereas cell a limit to how much could ever be seen using light.
surface membranes are partially permeable. All cells In order to understand why this is, it is necessary to
have a cell surface membrane. know something about the nature of light itself and to
understand the difference between magnification
■■ Vacuoles are not confined to plant cells; animal cells and resolution.
6 may have small vacuoles, such as phagocytic
vacuoles, although these are not usually
permanent structures. Magnification
Magnification is the number of times larger an image is,
We return to the differences between animal and plant than the real size of the object.
cells as seen using the electron microscope on page 13.
magnification = observed size of the image
Units of measurement actual size
or
In order to measure objects in the microscopic world, we M = I
A
need to use very small units of measurement, which are
unfamiliar to most people. According to international Here I = observed size of the image (that is, what you
agreement, the International System of Units (SI units) can measure with a ruler) and A = actual size (that is, the
should be used. In this system, the basic unit of length is real size – for example, the size of a cell before it
the metre (symbol, m). Additional units can be created is magnified).
in multiples of a thousand times larger or smaller, using
standard prefixes. For example, the prefix kilo means If you know two of these values, you can work out the
1000 times. Thus 1 kilometre = 1000 metres. The units third one. For example, if the observed size of the image
of length relevant to cell studies are shown in Table 1.1. and the magnification are known, you can work out the

actual size: A = I . If you write the formula in a triangle
M

Fraction of a metre Unit Symbol
one thousandth = 0.001 = 1/1000 = 10−3 millimetre mm
one millionth = 0.000 001 = 1/1000 000 = 10−6 micrometre μm
one thousand millionth = 0.000 000 001 = 1/1000 000 000 = 10−9 nanometre nm

Table 1.1  Units of measurement relevant to cell studies: μ is the Greek letter mu; 1 micrometre is a thousandth of a millimetre;
1 nanometre is a thousandth of a micrometre.

Chapter 1: Cell structure

as shown on the right and cover up the value you want to
find, it should be obvious how to do the right calculation.
I
Some worked examples are now provided. M ×A

WORKED EXAMPLE 1

Measuring cells a
Cells and organelles can be measured with a microscope 0 10 20 30 40 50 60 70 80 90 100
by means of an eyepiece graticule. This is a transparent
scale. It usually has 100 divisions (see Figure 1.8a). The
eyepiece graticule is placed in the microscope eyepiece
so that it can be seen at the same time as the object to
be measured, as shown in Figure 1.8b. Figure 1.8b shows
the scale over a human cheek epithelial cell. The cell
lies between 40 and 60 on the scale. We therefore say it
measures 20 eyepiece units in diameter (the difference
between 60 and 40). We will not know the actual size of
the eyepiece units until the eyepiece graticule scale is
calibrated.
To calibrate the eyepiece graticule scale, a miniature
transparent ruler called a stage micrometer scale is b
placed on the microscope stage and is brought into focus. cheek cells on a slide
This scale may be etched onto a glass slide or printed on on the stage of the
a transparent film. It commonly has subdivisions of 0.1 microscope
and 0.01 mm. The images of the two scales can then be 0 10 20 30 40 50 60 70 80 90 100 7

superimposed as shown in Figure 1.8c.
In the eyepiece graticule shown in the figure, 100 units
measure 0.25 mm. Hence, the value of each eyepiece
unit is:
0.25 = 0.0025 mm
100

Or, converting mm to μm:

0.25 × 1000 = 2.5 μm c eyepiece eyepiece
100 graticule graticule in
scale (arbitrary the eyepiece
The diameter of the cell shown superimposed on the scale units) of the
in Figure 1.8b measures 20 eyepiece units and so its actual microscope
diameter is:
20 × 2.5 μm = 50 μm

This diameter is greater than that of many human cells
because the cell is a flattened epithelial cell.

0 10 20 30 40 50 60 70 80 90 100

0 0.1 0.2
stage micrometer
Figure 1.8  Microscopical measurement. Three fields of view scale (marked in
seen using a high-power (× 40) objective lens. a An eyepiece 0.01mm and 0.1mm divisions)
graticule scale. b Superimposed images of human cheek
epithelial cells and the eyepiece graticule scale.
c Superimposed images of the eyepiece graticule scale
and the stage micrometer scale.

Cambridge International AS Level Biology

WORKED EXAMPLE 2

Calculating the magnification of a photograph a
or image
To calculate M, the magnification of a photograph or an
object, we can use the following method.
Figure 1.9 shows two photographs of a section
through the same plant cells. The magnifications of the two
photographs are the same. Suppose we want to know the
magnification of the plant cell labelled P in Figure 1.9b.
If we know its actual (real) length we can calculate its
magnification using the formula 
I
M = A

The real length of the cell is 80 μm.
Step 1  Measure the length in mm of the cell in the
photograph using a ruler. You should find that it is about
60 mm.
Step 2  Convert mm to μm. (It is easier if we first convert
all measurements to the same units – in this case
micrometres, μm.)

1 mm = 1000 μm
so 60 mm = 60 × 1000 μm
= 60 000 μm
Step 3  Use the equation to calculate the magnification. b

8 magnification, M image size, I
actual size, A
=

= 60 000 μm
80 μm
= × 750

The multiplication sign in front of the number 750 means
‘times’. We say that the magnification is ‘times 750’.

P

Figure 1.9  Photographs of the same types of plant
cells seen a with a light microscope, b with an electron
microscope, both shown at a magnification of about × 750.

QUESTION

1.2 a Calculate the magnification of the drawing of the
animal cell in Figure 1.4 on page 3.
Calculate the actual (real) length of the
b chloroplast labelled X in Figure 1.29 on page 21.

Chapter 1: Cell structure

WORKED EXAMPLE 3 BOX 1.1: Making temporary slides
Calculating magnification from a scale bar
Figure 1.10 shows a lymphocyte. Background information

6 µm Biological material may be examined live or in a preserved
state. Prepared slides contain material that has been killed
Figure 1.10  A lympho6cµymte. and preserved in a life-like condition. This material is often
We can calculate the magnification of the lymphocyte by cut into thin sections to enable light to pass through the
simply using the scale bar. All you need to do is measure structures for viewing with a light microscope. The sections
the length of the scale bar and then substitute this and the are typically stained and ‘mounted’ on a glass slide, forming
length it represents into the equation. a permanent preparation.
Step 1  Measure the scale bar. Here, it is 36 mm.
Step 2  Convert mm to μm: Temporary preparations of fresh material have the
36 mm = 36 × 1000 μm = 36 000 μm advantage that they can be made rapidly and are useful for
Step 3­  Use the equation to calculate the magnification: quick preliminary investigations. Sectioning and staining
may still be carried out if required. Sometimes macerated
magnification, M = image size, I (chopped up) material can be used, as when examining the 9
actual size, A structure of wood (xylem). A number of temporary stains are
36 000 μm commonly used. For example, iodine in potassium iodide
= 6 μm solution is useful for plant specimens. It stains starch blue-
black and will also colour nuclei and cell walls a pale yellow.
= × 6000 A dilute solution of methylene blue can be used to stain
animal cells such as cheek cells.
WORKED EXAMPLE 4
Viewing specimens yourself with a microscope will help
Calculating the real size of an object from its you to understand and remember structures more fully.
magnification This can be reinforced by making a pencil drawing on good
quality plain paper, using the guidance given later in
To calculate A, the real or actual size of an object, we can use Chapter 7 (Box 7.1, page 129). Remember always to draw
the following method. what you see, and not what you think you should see.

Figure 1.27 on page 19 shows parts of three plant cells Procedure
magnified × 5600. One of the chloroplasts is labelled
‘chloroplast’ in the figure. Suppose we want to know The material is placed on a clean glass slide and one or two
the actual length of this chloroplast. drops of stain added. A cover slip is carefully lowered over
Step 1  Measure the observed length of the image of the the specimen to protect the microscope lens and to help
chloroplast (I ) , in mm, using a ruler. The maximum length is prevent the specimen from drying out. A drop of glycerine
40 mm. mixed with the stain can also help prevent drying out.
Step 2  Convert mm to μm:
40 mm = 40 × 1000 μm = 40 000 μm Suitable animal material: human cheek cells
Step 3  Use the equation to calculate the actual length: Suitable plant material: onion epidermal cells, lettuce
epidermal cells, Chlorella cells, moss leaves

actual size, A = image size, I M
magnification,
40 000 μm
= 5600

= 7.1 μm (to one decimal place)

Cambridge International AS Level Biology

Resolution The electromagnetic spectrum
Look again at Figure 1.9 (page 8). Figure 1.9a is a light How is resolution linked with the nature of light? One
micrograph (a photograph taken with a light microscope, of the properties of light is that it travels in waves. The
also known as a photomicrograph). Figure 1.9b is an length of the waves of visible light varies, ranging from
electron micrograph of the same specimen taken at the about 400 nm (violet light) to about 700 nm (red light).
same magnification (an electron micrograph is a picture The human eye can distinguish between these different
taken with an electron microscope). You can see that wavelengths, and in the brain the differences are converted
Figure 1.9b, the electron micrograph, is much clearer. This to colour differences. (Colour is an invention of the brain!)
is because it has greater resolution. Resolution can be The whole range of different wavelengths is called the
defined as the ability to distinguish between two separate electromagnetic spectrum. Visible light is only one part of
points. If the two points cannot be resolved, they will be this spectrum. Figure 1.11 shows some of the parts of the
seen as one point. In practice, resolution is the amount electromagnetic spectrum. The longer the waves, the lower
of detail that can be seen – the greater the resolution, the their frequency (all the waves travel at the same speed, so
greater the detail. imagine them passing a post: shorter waves pass at higher
The maximum resolution of a light microscope is frequency). In theory, there is no limit to how short or how
200 nm. This means that if two points or objects are long the waves can be. Wavelength changes with energy:
closer together than 200 nm they cannot be distinguished the greater the energy, the shorter the wavelength.
as separate. Now look at Figure 1.12, which shows a mitochondrion,
It is possible to take a photograph such as Figure 1.9a some very small cell organelles called ribosomes (page 15)
and to magnify (enlarge) it, but we see no more detail; in and light of 400 nm wavelength, the shortest visible
other words, we do not improve resolution, even though wavelength. The mitochondrion is large enough to
we often enlarge photographs because they are easier to interfere with the light waves. However, the ribosomes
see when larger. With a microscope, magnification up to are far too small to have any effect on the light waves. The
10 the limit of resolution can reveal further detail, but any general rule is that the limit of resolution is about one half
further magnification increases blurring as well as the size the wavelength of the radiation used to view the specimen.
of the image. In other words, if an object is any smaller than half the
wavelength of the radiation used to view it, it cannot be
Resolution is the ability to distinguish between two seen separately from nearby objects. This means that the
objects very close together; the higher the resolution of an best resolution that can be obtained using a microscope
image, the greater the detail that can be seen. that uses visible light (a light microscope) is 200 nm,

Magnification is the number of times greater that an image since the shortest wavelength of visible light is 400 nm
is than the actual object; (violet light). In practice, this corresponds to a maximum
magnification = image size ÷ actual (real) size of the object. useful magnification of about 1500 times. Ribosomes are

approximately 25 nm in diameter and can therefore never
be seen using light.

X-rays infrared
gamma rays
microwaves

uv radio and TV waves

0.1 nm 10 nm 1000 nm 105 nm 107 nm 109 nm 1011 nm 1013 nm

visible light

400 nm 500 nm 600 nm 700 nm

violet blue green yellow orange red

Figure 1.11  Diagram of the electromagnetic spectrum (the waves are not drawn to scale). The numbers indicate the wavelengths
of the different types of electromagnetic radiation. Visible light is a form of electromagnetic radiation. The arrow labelled uv is
ultraviolet light.

Chapter 1: Cell structure

wavelength stained mitochondrion wavelength is extremely short (at least as short as that of
400 nm of diameter 1000nm X-rays). Second, because they are negatively charged, they
interferes with light waves can be focused easily using electromagnets (a magnet can
be made to alter the path of the beam, the equivalent of a
stained ribosomes of diameter 25nm glass lens bending light). 11
do not interfere with light waves
Figure 1.12  A mitochondrion and some ribosomes in the path Using an electron microscope, a resolution of 0.5 nm
of light waves of 400 nm length. can be obtained, 400 times better than a light microscope.

If an object is transparent, it will allow light waves to Transmission and scanning electron
pass through it and therefore will still not be visible. This microscopes
is why many biological structures have to be stained before
they can be seen. Two types of electron microscope are now in common use.
The transmission electron microscope, or TEM, was the
QUESTION type originally developed. Here the beam of electrons is
1.3 Explain why ribosomes are not visible using a light passed through the specimen before being viewed. Only
those electrons that are transmitted (pass through the
microscope. specimen) are seen. This allows us to see thin sections of
specimens, and thus to see inside cells. In the scanning
The electron microscope electron microscope (SEM), on the other hand, the
electron beam is used to scan the surfaces of structures,
Biologists, faced with the problem that they would never see and only the reflected beam is observed.
anything smaller than 200 nm using a light microscope,
realised that the only solution would be to use radiation of An example of a scanning electron micrograph is
a shorter wavelength than light. If you study Figure 1.11, shown in Figure 1.13. The advantage of this microscope is
you will see that ultraviolet light, or better still X-rays, that surface structures can be seen. Also, great depth of
look like possible candidates. Both ultraviolet and X-ray field is obtained so that much of the specimen is in focus
microscopes have been built, the latter with little success at the same time and a three-dimensional appearance
partly because of the difficulty of focusing X-rays. A much is achieved. Such a picture would be impossible to
better solution is to use electrons. Electrons are negatively obtain with a light microscope, even using the same
charged particles which orbit the nucleus of an atom. magnification and resolution, because you would have to
When a metal becomes very hot, some of its electrons keep focusing up and down with the objective lens to see
gain so much energy that they escape from their orbits, different parts of the specimen. The disadvantage of the
like a rocket escaping from Earth’s gravity. Free electrons SEM is that it cannot achieve the same resolution as
behave like electromagnetic radiation. They have a very a TEM. Using an SEM, resolution is between 3 nm
short wavelength: the greater the energy, the shorter the and 20 nm.
wavelength. Electrons are a very suitable form of radiation
for microscopy for two major reasons. Firstly, their Figure 1.13  False-colour scanning electron micrograph of the
head of a cat flea (× 100).

Cambridge International AS Level Biology

Viewing specimens with the electron To add to the difficulties of electron microscopy,
microscope the electron beam, and therefore the specimen and the
fluorescent screen, must be in a vacuum. If electrons
Figure 1.14 shows how an electron microscope works collided with air molecules, they would scatter, making it
and Figure 1.15 shows one in use. impossible to achieve a sharp picture. Also, water boils at
room temperature in a vacuum, so all specimens must be
It is not possible to see an electron beam, so to make dehydrated before being placed in the microscope. This
the image visible the electron beam has to be projected means that only dead material can be examined. Great
onto a fluorescent screen. The areas hit by electrons shine efforts are therefore made to try to preserve material in a
brightly, giving overall a black and white picture. The life-like state when preparing it for electron microscopy.
stains used to improve the contrast of biological specimens
for electron microscopy contain heavy metal atoms, which
stop the passage of electrons. The resulting picture is like
an X-ray photograph, with the more densely stained parts
of the specimen appearing blacker. ‘False-colour’ images
can be created by colouring the standard black and white
image using a computer.

electron gun and anode –
produce a beam of electrons
electron beam

vacuum
12

pathway of electrons
condenser electromagnetic
lens – directs the electron beam
onto the specimen

specimen is placed on a
grid

objective electromagnetic
lens – produces an image

projector electromagnetic Figure 1.15 A transmission electron microscope (TEM) in use.
lenses – focus the magni-

ed image onto the screen

screen or photographic
plate – shows the image of
the specimen
Figure 1.14 How an electron microscope (EM) works.

Chapter 1: Cell structure

Ultrastructure of an animal cell Figure 1.16 shows the appearance of typical animal cells
as seen with an electron microscope, and Figure 1.17 is a
The fine (detailed) structure of a cell as revealed by the diagram based on many other such micrographs.
electron microscope is called its ultrastructure.

cell surface
membrane

Golgi body

lysosome
mitochondria

13

nucleolus

endoplasmic
reticulum

nucleus

glycogen granules chromatin
microvillus

nuclear envelope

ribosomes

Figure 1.16  Representative animal cells as seen with a TEM. The cells are liver cells from a rat (× 9600). The nucleus is clearly
visible in one of the cells.

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centrosome with two centrioles close to the microvilli
nucleus and at right angles to each other Golgi vesicle
Golgi body
lysosome microtubules radiating from centrosome

mitochondrion ribosomes

cell surface membrane

rough endoplasmic reticulum

cytoplasm

nucleolus smooth endoplasmic reticulum
chromatin
nucleus nuclear pore

nuclear envelope
14 (two membranes)

Figure 1.17  Ultrastructure of a typical animal cell as seen with an electron microscope. In reality, the ER is more extensive than
shown, and free ribosomes may be more extensive. Glycogen granules are sometimes present in the cytoplasm.

QUESTION
1.4 Compare Figure 1.17 with Figure 1.4 on page 3. Name

the structures in an animal cell which can be seen
with the electron microscope but not with the light
microscope.

Structures and functions of organelles Figure 1.18  Transmission electron micrograph of the nucleus
of a cell from the pancreas of a bat (× 7500). The circular
Compartmentalisation and division of labour within the nucleus is surrounded by a double-layered nuclear envelope
cell are even more obvious with an electron microscope containing nuclear pores. The nucleolus is more darkly
than with a light microscope. We will now consider the stained. Rough ER (page 15) is visible in the surrounding
structures and functions of some of the cell components in cytoplasm.
more detail.

Nucleus

The nucleus (Figure 1.18) is the largest cell organelle. It
is surrounded by two membranes known as the nuclear
envelope. The outer membrane of the nuclear envelope is
continuous with the endoplasmic reticulum (Figure 1.17).

Chapter 1: Cell structure

The nuclear envelope has many small pores called nuclear of flattened compartments, called sacs, spreading 15
pores. These allow and control exchange between the throughout the cell. Processes can take place inside these
nucleus and the cytoplasm. Examples of substances leaving sacs, separated from the cytoplasm. The sacs can be
the nucleus through the pores are mRNA and ribosomes interconnected to form a complete system (reticulum) –
for protein synthesis. Examples of substances entering the connections have been compared to the way in which
through the nuclear pores are proteins to help make the different levels of a parking lot are connected by
ribosomes, nucleotides, ATP (adenosine triphosphate) and ramps. The ER is continuous with the outer membrane of
some hormones such as thyroid hormone T3. the nuclear envelope (Figure 1.17).

Within the nucleus, the chromosomes are in a loosely There are two types of ER: rough ER and smooth ER.
coiled state known as chromatin (except during nuclear Rough ER is so called because it is covered with many tiny
division, Chapter 5). Chromosomes contain DNA, which is organelles called ribosomes. These are just visible as black
organised into functional units called genes. Genes control dots in Figures 1.18 and 1.19. At very high magnifications
the activities of the cell and inheritance; thus the nucleus they can be seen to consist of two subunits: a large and a
controls the cell’s activities. When a cell is about to divide, small subunit. Ribosomes are the sites of protein synthesis
the nucleus divides first so that each new cell will have its (page 119). They can be found free in the cytoplasm as well
own nucleus (Chapters 5 and 16). Also within the nucleus, as on the rough ER. They are very small, only about 25 nm
the nucleolus makes ribosomes, using the information in in diameter. They are made of RNA (ribonucleic acid) and
its own DNA. protein. Proteins made by the ribosomes on the rough ER
enter the sacs and move through them. The proteins are
Endoplasmic reticulum and ribosomes often modified in some way on their journey. Small sacs
called vesicles can break off from the ER and these can
When cells were first seen with the electron microscope, join together to form the Golgi body. They form part of the
biologists were amazed to see so much detailed structure. secretory pathway because the proteins can be exported
The existence of much of this had not been suspected. This from the cell via the Golgi vesicles (Figure 1.2).
was particularly true of an extensive system of membranes
running through the cytoplasm, which became known Smooth ER, so called because it lacks ribosomes, has a
as the endoplasmic reticulum (ER) (Figures 1.18, 1.19 completely different function. It makes lipids and steroids,
and 1.22). The membranes form an extended system such as cholesterol and the reproductive hormones
oestrogen and testosterone.
Figure 1.19  Transmission electron micrograph of rough ER
covered with ribosomes (black dots) (× 17 000). Some free Golgi body (Golgi apparatus or Golgi
ribosomes can also be seen in the cytoplasm on the left. complex)

The Golgi body is a stack of flattened sacs (Figure 1.20).
More than one Golgi body may be present in a cell. The
stack is constantly being formed at one end from vesicles
which bud off from the ER, and broken down again at the
other end to form Golgi vesicles. The stack of sacs together
with the associated vesicles is referred to as the Golgi
apparatus or Golgi complex.

The Golgi body collects, processes and sorts molecules
(particularly proteins from the rough ER), ready for
transport in Golgi vesicles either to other parts of the cell
or out of the cell (secretion). Two examples of protein
processing in the Golgi body are the addition of sugars
to proteins to make molecules known as glycoproteins,
and the removal of the first amino acid, methionine, from
newly formed proteins to make a functioning protein.
In plants, enzymes in the Golgi body convert sugars into
cell wall components. Golgi vesicles are also used to
make lysosomes.

Cambridge International AS Level Biology

Mitochondria

Structure
The structure of the mitochondrion as seen with the
electron microscope is visible in Figures 1.16, 1.22, 12.13
and 12.14. Mitochondria (singular: mitochondrion)
are usually about 1 μm in diameter and can be various
shapes, often sausage-shaped as in Figure 1.22. They are
surrounded by two membranes (an envelope). The inner
of these is folded to form finger-like cristae which project
Figure 1.20  Transmission electron micrograph of a Golgi body. into the interior solution, or matrix. The space between the
A central stack of saucer-shaped sacs can be seen budding two membranes is called the intermembrane space. The
off small Golgi vesicles (green). These may form secretory outer membrane contains a transport protein called porin,
which forms wide aqueous channels allowing easy access
of small, water-soluble molecules from the surrounding
cytoplasm into the intermembrane space. The inner
vesicles whose contents can be released at the cell surface by membrane is a far more selective barrier and controls
exocytosis (page 87). precisely what ions and molecules can enter the matrix.

16 Lysosomes The number of mitochondria in a cell is very variable.
As they are responsible for aerobic respiration, it is not
Lysosomes (Figure 1.21) are spherical sacs, surrounded surprising that cells with a high demand for energy,
by a single membrane and having no internal structure. such as liver and muscle cells, contain large numbers of
They are commonly 0.1– 0.5 μm in diameter. They contain mitochondria. A liver cell may contain as many as 2000
digestive (hydrolytic) enzymes which must be kept mitochondria. If you exercise regularly, your muscles will
separate from the rest of the cell to prevent damage from make more mitochondria.
being done. Lysosomes are responsible for the breakdown
(digestion) of unwanted structures such as old organelles Function of mitochondria and the role of ATP
or even whole cells, as in mammary glands after lactation
(breast feeding). In white blood cells, lysosomes are used As we have seen, the main function of mitochondria is
to digest bacteria (see endocytosis, page 87). Enzymes are to carry out aerobic respiration, although they do have
sometimes released outside the cell – for example, in the other functions, such as the synthesis of lipids. During

replacement of cartilage with bone during development.
The heads of sperm contain a special lysosome, the
acrosome, for digesting a path to the ovum (egg).

Figure 1.21  Lysosomes (orange) in a mouse kidney cell Figure 1.22  Mitochondrion (orange) with its double
(× 55 000). They contain cell structures in the process of membrane (envelope); the inner membrane is folded to form
digestion, and vesicles (green). Cytoplasm is coloured blue here. cristae (× 20 000). Mitochondria are the sites of aerobic cell
respiration. Note also the rough ER.

Chapter 1: Cell structure

respiration, a series of reactions takes place in which Cell surface membrane 17
energy is released from energy-rich molecules such as
sugars and fats. Most of this energy is transferred to The cell surface membrane is extremely thin (about 7 nm).
molecules of ATP. ATP (adenosine triphosphate) is the However, at very high magnifications, at least × 100 000, it
energy-carrying molecule found in all living cells. It is can be seen to have three layers, described as a trilaminar
known as the universal energy carrier. appearance. This consists of two dark lines (heavily
stained) either side of a narrow, pale interior (Figure
The reactions of respiration take place in solution in the 1.23). The membrane is partially permeable and controls
matrix and in the inner membrane (cristae). The matrix exchange between the cell and its environment. Membrane
contains enzymes in solution, including those of the Krebs structure is discussed further in Chapter 4.
cycle (Chapter 12) and these supply the hydrogen and
electrons to the reactions that take place in the cristae. Figure 1.23  Cell surface membrane (× 250 000). At this
The flow of electrons along the precisely placed electron magnification the membrane appears as two dark lines at the
carriers in the membranes of the cristae is what provides edge of the cell.
the power to generate ATP molecules, as explained
in Chapter 12. The folding of the cristae increases the Microvilli
efficiency of respiration because it increases the surface
area available for these reactions to take place. Microvilli (singular: microvillus) are finger-like extensions
of the cell surface membrane, typical of certain epithelial
Once made, ATP leaves the mitochondrion and, as it is cells (cells covering surfaces of structures). They greatly
a small, soluble molecule, it can spread rapidly to all parts increase the surface area of the cell surface membrane
of the cell where energy is needed. Its energy is released (Figure 1.17 on page 14). This is useful, for example, for
by breaking the molecule down to ADP (adenosine absorption in the gut and for reabsorption in the proximal
diphosphate). This is a hydrolysis reaction. The ADP can convoluted tubules of the kidney (page 308).
then be recycled into a mitochondrion for conversion back
to ATP during aerobic respiration. Microtubules and microtubule organising
centres (MTOCs)
The endosymbiont theory
Microtubules are long, rigid, hollow tubes found in the
In the 1960s, it was discovered that mitochondria and cytoplasm. They are very small, about 25 nm in diameter.
chloroplasts contain ribosomes which are slightly smaller Together with actin filaments and intermediate filaments
than those in the cytoplasm and are the same size as those (not discussed in this book), they make up the cytoskeleton,
found in bacteria. The size of ribosomes is measured in an essential structural component of cells which helps to
‘S units’, which are a measure of how fast they sediment determine cell shape.
in a centrifuge. Cytoplasmic ribosomes are 80S, while
those of bacteria, mitochondria and ribosomes are 70S. Microtubules are made of a protein called tubulin.
It was also discovered in the 1960s that mitochondria Tubulin has two forms, α-tubulin (alpha-tubulin) and
and chloroplasts contain small, circular DNA molecules, β-tubulin (beta-tubulin). α- and β-tubulin molecules
also like those found in bacteria. It was later proved that combine to form dimers (double molecules). These dimers
mitochondria and chloroplasts are, in effect, ancient are then joined end to end to form long ‘protofilaments’.
bacteria which now live inside the larger cells typical This is an example of polymerisation. Thirteen
of animals and plants (see prokaryotic and eukaryotic protofilaments then line up alongside each other in a ring
cells, page 21). This is known as the endosymbiont to form a cylinder with a hollow centre. This cylinder is
theory. ‘Endo’ means ‘inside’ and a ‘symbiont’ is an the microtubule. Figure 1.24 (overleaf) shows the
organism which lives in a mutually beneficial relationship helical pattern formed by neighbouring α- and
with another organism. The DNA and ribosomes of β-tubulin molecules.
mitochondria and chloroplasts are still active and
responsible for the coding and synthesis of certain vital
proteins, but mitochondria and chloroplasts can no longer
live independently.

Mitochondrial ribosomes are just visible as tiny dark
orange dots in the mitochondrial matrix in Figure 1.22.

Cambridge International AS Level Biology

Apart from their mechanical function of support, microtubule organising centres (MTOCs). These are
microtubules have a number of other functions. Secretory discussed further in the following section on centrioles.
vesicles and other organelles and cell components can be Because of their simple construction, microtubules can
moved along the outside surfaces of the microtubules, be formed and broken down very easily at the MTOCs,
forming an intracellular transport system. Membrane- according to need.
bound organelles are held in place by the cytoskeleton.
During nuclear division (Chapter 5), the spindle used for Centrioles and centrosomes
the separation of chromatids or chromosomes is made of
microtubules, and microtubudliemsefrorm part of the structure The extra resolution of the electron microscope reveals
of centrioles. that just outside the nucleus of animal cells there are
The assembly of microtubules from tubulin really two centrioles and not one as it appears under the
molecules is controlled by spdeicmiaelr locations i5nncmells called light microscope (compare Figures 1.4 and 1.17). They lie
close together and at right angles to each other in a region
a dimer known as the centrosome. Centrioles and the centrosome
are absent from most plant cells.
5 nm 25 nm
A centriole is a hollow cylinder about 500 nm long,
dimers can reversibly app5enamrance in 25nm formed from a ring of short microtubules. Each centriole
attach to a microtubule cross section contains nine triplets of microtubules (Figures 1.25
and 1.26).

dimers can reversibly appearance in 25nm triplet of microtubules (one
attach to a microtubule cross section complete microtubule and
dimers can reversibly appearance in two partial microtubules)
attach to a microtubule cross section

18 The dimers form 13 proto laments 500 nm
The dimers have a around a hollow core. 200 nm
helical arrangement. The dimers form 13 proto laments
The dimers have a around a hollow core.
hbelical arrangement. The dimers form 13 proto laments
The dimers have a around a hollow core.
helical arrangement.

Figure 1.25 The structure of a centriole. It consists of nine
groups of microtubules arranged in triplets.

Figure 1.24 a The structure of a microtubule and b the Figure 1.26 Centrioles in transverse and longitudinal section
arrangement of microtubules in two cells. The microtubules (TS and LS) (× 86 000). The one on the left is seen in TS and
are coloured yellow. clearly shows the nine triplets of microtubules which make up
the structure.

Chapter 1: Cell structure

The function of the centrioles remains a mystery. Until Chloroplasts
recently, it was believed that they acted as MTOCs for the
assembly of the microtubules that make up the spindle The structure of the chloroplast as seen with the electron
during nuclear division (Chapter 5). It is now known that microscope is visible in Figures 1.27–1.29 and at a
this is done by the centrosome, but does not involve higher resolution in Figure 13.6. Chloroplasts tend to
the centrioles. have an elongated shape and a diameter of about 3 to
10 μm (compare 1 μm diameter for mitochondria). Like
Centrioles found at the bases of cilia (page 189) and mitochondria, they are surrounded by two membranes,
flagella, where they are known as basal bodies, do act as forming the chloroplast envelope. Also like mitochondria,
MTOCs. The microtubules that extend from the basal chloroplasts replicate themselves independently of cell
bodies into the cilia and flagella are essential for the division by dividing into two.
beating movements of these organelles.
The main function of chloroplasts is to carry
Ultrastructure of a plant cell out photosynthesis. Chloroplasts are an excellent
example of how structure is related to function, so a
All the structures so far described in animal cells are also brief understanding of their function will help you to
found in plant cells, with the exception of centrioles and understand their structure.
microvilli. The plant cell structures that are not found in
animal cells are the cell wall, the large central vacuole, and During the first stage of photosynthesis (the
chloroplasts. These are all shown clearly in Figures 1.27 light dependent stage) light energy is absorbed by
and 1.28. The structures and functions of cell walls and photosynthetic pigments, particularly the green pigment
vacuoles have been described on page 5. chlorophyll. Some of this energy is used to manufacture
ATP from ADP. An essential stage in the process is the

ribosome 19
cell surface
nuclear envelope membrane
heterochromatin
euchromatin vacuole
tonoplast
nucleolus

nuclear pore

chloroplast

cell wall
endoplasmic
reticulum

mitochondrion
starch grain
Golgi body

Figure 1.27  A representative plant cell as seen with a TEM. The cell is a palisade cell from a soya bean leaf (× 5600).

Cambridge International AS Level Biology

splitting of water into hydrogen and oxygen. The hydrogen mitochondria). The sugars made may be stored in the form
is used as the fuel which is oxidised to provide the energy of starch grains in the stroma (Figures 1.27 and 13.6). The
to make the ATP. This process, as in mitochondria, lipid droplets also seen in the stroma as black spheres in
requires electron transport in membranes. This explains electron micrographs (Figure 1.29) are reserves of lipid for
why chloroplasts contain a complex system of membranes. making membranes or from the breakdown of membranes
in the chloroplast.
The membrane system is highly organised. It consists
of fluid-filled sacs called thylakoids which spread out like Like mitochondria, chloroplasts have their own protein
sheets in three dimensions. In places, the thylakoids form synthesising machinery, including 70S ribosomes and
flat, disc-like structures that stack up like piles of coins a circular strand of DNA. In electron micrographs, the
many layers deep, forming structures called grana (from ribosomes can just be seen as small black dots in the
their appearance in the light microscope; ‘grana’ means stroma (Figure 13.6, page 291). Fibres of DNA can also
grains). These membranes contain the photosynthetic sometimes be seen in small, clear areas in the stroma.
pigments and electron carriers needed for the light
dependent stage of photosynthesis. Both the membranes As with mitochondria, it has been shown that
and whole chloroplasts can change their orientation chloroplasts originated as endosymbiotic bacteria, in this
within the cell in order to receive the maximum amount case photosynthetic blue-green bacteria. The endosymbiont
of light. theory is discussed in more detail on page 17.

The second stage of photosynthesis (the light QUESTION
independent stage) uses the energy and reducing power 1.5 Compare Figure 1.28 with Figure 1.5 on page 4. Name
generated during the first stage to convert carbon dioxide
into sugars. This requires a cycle of enzyme-controlled the structures in a plant cell which can be seen
reactions called the Calvin cycle and takes place in with the electron microscope but not with the light
solution in the stroma (the equivalent of the matrix in microscope.

20

middle lamella chloroplast
plasmodesma cytoplasm
Golgi body

cell walls of Golgi
neighbouring cells vesicle

vacuole tonoplast
cell sap

mitochondrion
smooth ER

cell surface
membrane
(pressed against
cell wall)

ribosomes

nucleus nuclear pore envelope grana
nucleolus chloroplast
chromatin rough ER
nuclear envelope microtubule

Figure 1.28  Ultrastructure of a typical plant cell as seen with the electron microscope. In reality, the ER is more extensive than
shown. Free ribosomes may also be more extensive.

Chapter 1: Cell structure

additional structures structures always
sometimes present present

X agellum cell wall
for locomotion; containing
Figure 1.29  Chloroplasts (× 16 000). Thylakoids (yellow) run very simple structure murein, a
through the stroma (dark green) and are stacked in places capsule peptidoglycan
to form grana. Black circles among the thylakoids are lipid additional protection cell surface
droplets. See also Figure 13.6, page 291. Chloroplast X is membrane
referred to in Question 1.2. infolding of cell
surface membrane cytoplasm
Two fundamentally different may form a
types of cell photosynthetic
membrane or carry
At one time it was common practice to try to classify out nitrogen xation
all living organisms as either animals or plants. With
advances in our knowledge of living things, it has plasmid circular DNA
become obvious that the living world is not that simple. small circle of DNA; sometimes referred
Fungi and bacteria, for example, are very different from several may to as a chromosome
animals and plants, and from each other. Eventually it be present ribosomes
was discovered that there are two fundamentally different pili
types of cell. The most obvious difference between for attachment to 21
these types is that one possesses a nucleus and the other other cells or surfaces;
does not. involved in sexual
reproduction
Organisms that lack nuclei are called prokaryotes
(‘pro’ means before; ‘karyon’ means nucleus). They are, Figure 1.30  Diagram of a generalised bacterium showing the
on average, about 1000 to 10 000 times smaller in volume typical features of a prokaryotic cell.
than cells with nuclei, and are much simpler in structure –
for example, their DNA lies free in the cytoplasm. QUESTION
1.6 List the structural features that prokaryotic and
Organisms whose cells possess nuclei are called
eukaryotes (‘eu’ means true). Their DNA lies inside a eukaryotic cells have in common. Briefly explain why
nucleus. Eukaryotes include animals, plants, fungi and each of the structures you have listed is essential.
a group containing most of the unicellular eukaryotes
known as protoctists. Most biologists believe that Viruses
eukaryotes evolved from prokaryotes, 1500 million years
after prokaryotes first appeared on Earth. We mainly study In 1852, a Russian scientist discovered that certain diseases
animals and plants in this book, but all eukaryotic cells could be transmitted by agents that, unlike bacteria, could
have certain features in common. pass through the finest filters. This was the first evidence
for the existence of viruses, tiny ‘organisms’ which are
A generalised prokaryotic cell is shown in Figure 1.30. much smaller than bacteria and are on the boundary
A comparison of prokaryotic and eukaryotic cells is given between what we think of as living and non-living. Unlike
in Table 1.2. prokaryotes and eukaryotes, viruses do not have a cell
structure. In other words, they are not surrounded by
a partially permeable membrane containing cytoplasm
with ribosomes. They are much simpler in structure. Most
consist only of:

■■ a self-replicating molecule of DNA or RNA which acts
as its genetic code

■■ a protective coat of protein molecules.

Cambridge International AS Level Biology

Prokaryotes Eukaryotes

average diameter of cell is 0.5–5 μm cells commonly up to 40 μm diameter and commonly 1000–10 000 times the volume
of prokaryotic cells

DNA is circular and lies free in the DNA is not circular and is contained in a nucleus – the nucleus is surrounded by an
cytoplasm envelope of two membranes

DNA is naked DNA is associated with protein, forming structures called chromosomes
slightly smaller (70S) ribosomes (about slightly larger (80S) ribosomes (about 25 nm diameter) than those of prokaryotes
20 nm diameter) than those of eukaryotes ER present, to which ribosomes may be attached
no ER present many types of cell organelle present (extensive compartmentalisation and division
of labour):
very few cell organelles – no separate ■  some organelles are bounded by a single membrane, e.g. lysosomes, Golgi body,
membrane-bound compartments unless
formed by infolding of the cell surface vacuoles
membrane ■  some are bounded by two membranes (an envelope), e.g. nucleus,

cell wall present – wall contains murein, mitochondrion, chloroplast
a peptidoglycan (a polysaccharide ■  some have no membrane, e.g. ribosomes, centrioles, microtubules
combined with amino acids) cell wall sometimes present, e.g. in plants and fungi – contains cellulose or lignin in
plants, and chitin (a nitrogen-containing polysaccharide similar to cellulose) in fungi

Table 1.2  A comparison of prokaryotic and eukaryotic cells.

Figure 1.31 shows the structure of a simple virus. It has capsid
22 a very symmetrical shape. Its protein coat (or capsid) is protein
molecules
made up of separate protein molecules, each of which is
called a capsomere. DNA or RNA
genetic code
Viruses range in size from about 20–300 nm (about 50
times smaller on average than bacteria).

All viruses are parasitic because they can only
reproduce by infecting and taking over living cells. The
virus DNA or RNA takes over the protein synthesising
machinery of the host cell, which then helps to make new
virus particles.

Figure 1.31  The structure of a simple virus.

Summary ■■ With a light microscope, cells may be measured using

■■ The basic unit of life, the cell, can be seen clearly only an eyepiece graticule and a stage micrometer. Using
with the aid of microscopes. The light microscope uses I
light as a source of radiation, whereas the electron the formula A = M the actual size of an object (A) or its
microscope uses electrons. The electron microscope has
greater resolution (allows more detail to be seen) than magnification (M) can be found if its observed (image)
the light microscope, because electrons have a shorter
wavelength than light. size (I) is measured and A or M, as appropriate, is known.

■■ All cells are surrounded by a partially permeable cell
surface membrane that controls exchange between
the cell and its environment. All cells contain genetic
material in the form of DNA, and ribosomes for
protein synthesis.

Chapter 1: Cell structure

■■ The simplest cells are prokaryotic cells, which are ■■ The cytoplasm of eukaryotic cells contains many
thought to have evolved before, and given rise to, the membrane-bound organelles providing separate
much more complex and much larger eukaryotic cells. compartments for specialised activities (division
Prokaryotic cells lack a true nucleus and have smaller of labour). Organelles of eukaryotic cells include
(70S) ribosomes than eukaryotic cells. They also lack endoplasmic reticulum (ER), 80S ribosomes,
membrane-bound organelles. Their DNA is circular and mitochondria, Golgi apparatus and lysosomes. Animal
lies naked in the cytoplasm. cells also contain a centrosome and centrioles. Plant
cells may contain chloroplasts, often have a large,
■■ All eukaryotic cells possess a nucleus containing one or permanent, central vacuole and have a cell wall
more nucleoli and DNA. The DNA is linear and bound to containing cellulose.
proteins to form chromatin.

End-of-chapter questions

1 Which one of the following cell structures can be seen with a light microscope? [1]
A mitochondrion
B ribosome 23
C rough ER
D smooth ER [1]
[1]
2 The use of electrons as a source of radiation in the electron microscope allows high resolution to be achieved
because electrons: [8]
A are negatively charged.
B can be focused using electromagnets.
C have a very short wavelength.
D travel at the speed of light.

3 Which one of the following structures is found in animal cells, but not in plant cells?
A cell surface membrane
B centriole
C chloroplast
D Golgi body

4 Copy and complete the following table, which compares light microscopes
with electron microscopes. Some boxes have been filled in for you.

Feature Light microscope Electron microscope
source of radiation
wavelength of radiation used glass about 0.005 nm
maximum resolution coloured dyes 0.5 nm in practice
lenses coloured
specimen non-living or dead
stains
image

Cambridge International AS Level Biology

5 List ten structures you could find in an electron micrograph of an animal cell which would be absent from the [10]
cell of a bacterium.

6 Advice on answering question 6: If you are asked to distinguish between two things, it is likely that it is
because they have certain things in common and that they may even be confused with each other. In your answer
it is helpful where relevant to point out similarities as well as differences. Remember that for organelles there may
be differences in both structure and function.

Distinguish between the following pairs of terms: [3]
[2]
a magnification and resolution [4]
b light microscope and electron microscope [3]
c nucleus and nucleolus [3]
d chromatin and chromosome [4]
e membrane and envelope [4]
f smooth ER and rough ER [Total: 23]
g prokaryote and eukaryote

7 List: [9]
a three organelles each lacking a boundary membrane [12]
b three organelles each bounded by a single membrane
c three organelles each bounded by two membranes (an envelope)

24 8 Identify each cell structure or organelle from its description below.
a manufactures lysosomes
b manufactures ribosomes
c site of protein synthesis
d can bud off vesicles which form the Golgi body
e can transport newly synthesised protein round the cell
f manufactures ATP in animal and plant cells
g controls the activity of the cell, because it contains the DNA
h carries out photosynthesis
i can act as a starting point for the growth of spindle microtubules during cell division
j contains chromatin
k partially permeable barrier only about 7nm thick
l organelle about 25nm in diameter

9 The electron micrograph on page 25 shows part of a secretory cell from the pancreas. The secretory vesicles
are Golgi vesicles and appear as dark round structures. The magnification is × 8000.
a Copy and complete the table. Use a ruler to help you find the actual sizes of the structures. Give your
answers in micrometres.

Structure Observed diameter Actual size
(measured with ruler)
maximum diameter of a Golgi vesicle
maximum diameter of nucleus
maximum length of the labelled mitochondrion

[9]

Chapter 1: Cell structure

b Make a fully labelled drawing of representative parts of the cell. You do not have to draw everything, but [14]
enough to show the structures of the main organelles. Use a full page of plain paper and a sharp pencil. Use [1]
Figures 1.16 and 1.17 in this book and the simplified diagram in d below to help you identify the structures.

c The mitochondria in pancreatic cells are mostly sausage-shaped in three dimensions. Explain why some of the
mitochondria in the electron micrograph below appear roughly circular.

mitochondrion

secretory vesicle

25

d The figure below shows a diagram based on an electron micrograph of a secretory cell from the pancreas.
This type of cell is specialised for secreting (exporting) proteins. Some of the proteins are digestive enzymes of
the pancreatic juice. The cell is very active, requiring a lot of energy. The arrows show the route taken by the
protein molecules.

A magni ed

EA C protein (enzyme)
B D molecules

i Describe briefly what is happening at each of the stages A, B, C and D. [8]
ii Name one molecule or structure which leaves the nucleus by route E. [1]
iii Through which structure must the molecule or structure you named in ii pass to get through the
[1]
nuclear envelope? [1]
iv Name the molecule which leaves the mitochondrion in order to provide energy for this cell. [Total: 35]

Cambridge International AS Level Biology

10 One technique used to investigate the activity of cell organelles is called differential centrifugation. In this [1]
technique, a tissue is homogenised (ground in a blender), placed in tubes and spun in a centrifuge. This makes [4]
organelles sediment (settle) to the bottom of the tubes. The larger the organelles, the faster they sediment.
By repeating the process at faster and faster speeds, the organelles can be separated from each other according
to size. Some liver tissue was treated in this way to separate ribosomes, nuclei and mitochondria. The centrifuge
was spun at 1000 g, 10 000 g or 100 000 g (‘g ’ is gravitational force).

a In which of the three sediments – 1000g, 10000g or 100000g – would you expect to find the following?

i ribosomes

ii nuclei

iii mitochondria

b Liver tissue contains many lysosomes. Suggest why this makes it difficult to study mitochondria using the
differential centrifugation technique.

[Total: 5]

26

27 27

Chapter 2:

Biological molecules

Learning outcomes ■ carry out biochemical tests to identify
carbohydrates, lipids and proteins
You should be able to:
■ explain some key properties of water that make
■ describe how large biological molecules are life possible
made from smaller molecules

■ describe the structure and function of
carbohydrates, lipids and proteins

Cambridge International AS Level Biology

‘And the winner is …’

Nobel prizes were first awarded in 1901. The prizes of excellence for technologies associated with biology,
were founded by Alfred Nobel, the inventor of particularly in the pharmaceutical and computing
dynamite. The winning scientists are referred to as industries. Scientists from many disciplines and
Nobel laureates. from all over the world have the opportunity to
The study of biological molecules has been so work together in a close-knit and highly productive
important in the last 100 years that it has inevitably community.
led to the award of many Nobel prizes. Many of the
winners have been associated with the University
of Cambridge.
For example, William and Lawrence Bragg (father
and son) won the Physics prize in 1915 for work
on X-ray crystallography, which was to lead to the
discovery of the structure of key biological molecules.
Frederick Sanger won prizes in 1958 and 1980 for work
on sequencing the subunits of proteins and nucleic
acids. James Watson and Francis Crick, along with
Maurice Wilkins from King’s College London, won
the 1962 prize for Physiology and Medicine for their
discovery of the structure of DNA in 1953, arguably
one of the most important scientific discoveries of
all time. John Kendrew and Max Perutz received
the Chemistry prize in the same year for their work
on the three-dimensional structure of the proteins
28 myoglobin (Figure 2.1) and haemoglobin, essential for

an understanding of how proteins function. Figure 2.1  Kendrew’s original model of the myoglobin
Not surprisingly, Cambridge has become a centre
molecule, made in 1957.

The study of biological molecules forms an important functions. This will become clear in this chapter and in
branch of biology known as molecular biology. The Chapter 3. Our understanding of how structure is related
importance of the subject is clear from the relatively large to function may lead to the creation of a vast range of
number of Nobel prizes that have been awarded in this ‘designer’ molecules to carry out such varied functions as
field. It has attracted some of the best scientists, even from large-scale industrial reactions and precise targeting of
other disciplines like physics and mathematics. cells in medical treatment.

Molecular biology is closely linked with biochemistry, The building blocks of life
which looks at the chemical reactions of biological
molecules. The sum total of all the biochemical reactions The four most common elements in living organisms
in the body is known as metabolism. Metabolism is are, in order of abundance, hydrogen, carbon, oxygen
complex, but it has an underlying simplicity. For example, and nitrogen. They account for more than 99% of the
there are only 20 common amino acids used to make atoms found in all living things. Carbon is particularly
naturally occurring proteins, whereas theoretically there important because carbon atoms can join together to form
could be millions. Why so few? One possibility is that all long chains or ring structures. They can be thought of as the
the manufacture and reactions of biological molecules basic skeletons of organic molecules to which groups
must be controlled and regulated and, the more there of other atoms are attached. Organic molecules always
are, the more complex the control becomes. (Control and contain carbon and hydrogen.
regulation by enzymes is examined in Chapter 3.)
It is believed that, before life evolved, there was a
Another striking principle of molecular biology is how period of chemical evolution in which thousands of
closely the structures of molecules are related to their carbon-based molecules evolved from the more simple

Chapter 2: Biological molecules

molecules that existed on the young planet Earth. Such Natural examples of polymers are cellulose and
an effect can be artificially created reasonably easily rubber. There are many examples of industrially produced
today given similar raw ingredients, such as methane polymers, such as polyester, polythene, PVC (polyvinyl
n((dCHiitsH2rcSoh4)g)a,,eracngnae(dr.NbTao2hn)n,eesadnemieosrmxigmidoypneslioe(aCub(rOuNct2eH)k,–e3h)yfyoadbrnireodoxlgohaegymnidcp(raHloleg,m2e)a,nonwlseeauclteluefcirldter(seHi,ca2Ol ), chloride) and nylon. All these are made up of carbon-based
which are relatively limited in variety, then act as the monomers and contain thousands of carbon atoms joined
building blocks for larger molecules. The main ones are end to end.
shown in Figure 2.2.
We shall now take a closer look at some of the small
Figure 2.2  The building blocks of life. biological molecules and the larger molecules made from
them. Organic bases, nucleotides and nucleic acids are
Monomers, polymers and dealt with in Chapter 6.
macromolecules
Carbohydrates
The term macromolecule means giant molecule. There are
three types of macromolecule in living organisms, namely All carbohydrates contain the elements carbon, hydrogen
polysaccharides, proteins (polypeptides) and nucleic acids and oxygen. The ‘hydrate’ part of the name comes from
(polynucleotides). The prefix ‘poly’ means many, and these the fact that hydrogen and oxygen atoms are present in the
molecules are polymers, meaning that they are made up ratio of 2 : 1, as they are in water (‘hydrate’ refers to water).
of many repeating subunits that are similar or identical to The general formula for a carbohydrate can therefore be
each other. These subunits are referred to as monomers. wriCtteanrbaoshCydx(rHat2eOs )ayr.e divided into three main
They are joined together like beads on a string. Making groups, namely monosaccharides, disaccharides and
such molecules is relatively simple because the same polysaccharides. The word ‘saccharide’ refers to a sugar or
reaction is repeated many times. sweet substance.

The monomers from which polysaccharides, proteins Monosaccharides 29
and nucleic acids are made are monosaccharides, Monosaccharides are sugars. Sugars dissolve easily in
amino acids and nucleotides respectively, as shown in water to form sweet-tasting solutions. Monosaccharides
Figure 2.2. Figure 2.2 also shows two types of molecule shuagvaerthmeogleecnuelreal(‘fmoromnou’lam(eCaHns2Oon)ne)a.nTdhceomnsaiisnt of a single
which, although not polymers, are made up of simpler types of
biochemicals. These are lipids and nucleotides. monosaccharides, if they are classified according to the
number of carbon atoms in each molecule, are trioses
(3C), pentoses (5C) and hexoses (6C). The names of all
sugars end with -ose. Common hexoses are glucose,
fructose and galactose. Two common pentoses are ribose
and deoxyribose.

A macromolecule is a large biological molecule such as
a protein, polysaccharide or nucleic acid.
A monomer is a relatively simple molecule which is
used as a basic building block for the synthesis of
a polymer; many monomers are joined together to
make the polymer, usually by condensation reactions;
common examples of molecules used as monomers are
monosaccharides, amino acids and nucleotides.
A polymer is a giant molecule made from many similar
repeating subunits joined together in a chain; the
subunits are much smaller and simpler molecules
known as monomers; examples of biological polymers
are polysaccharides, proteins and nucleic acids.

Cambridge International AS Level Biology

Molecular and structural formulae Ring structures

The formula for a hexose can be written as C6H12O6. One important aspect of the structure of pentoses and
This is known as the molecular formula. It is also useful hexoses is that the chain of carbon atoms is long enough
to show the arrangements of the atoms, which can be to close up on itself and form a more stable ring structure.
done using a diagram known as the structural formula. This can be illustrated using glucose as an example. When
Figure 2.3 shows the structural formula of glucose, a glucose forms a ring, carbon atom number 1 joins to the
hexose, which is the most common monosaccharide. oxygen on carbon atom number 5 (Figure 2.4). The ring
therefore contains oxygen, and carbon atom number 6 is
HH not part of the ring.

CO CO You will see from Figure 2.4 that the hydroxyl group,
–OH, on carbon atom 1 may be above or below the
HC 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) and the
HOC H more HO C H form where it is above the ring is β-glucose (beta-glucose).
commonly The same molecule can switch between the two forms.
H C O H shown as Two forms of the same chemical are known as isomers,
H C OH and the extra variety provided by the existence of α- and
β-isomers has important biological consequences, as
HC OH H C OH we shall see in the structures of starch, glycogen
and cellulose.

HC OH CH2OH QUESTION
2.1 The formula for a hexose is C6H12O6 or (CH2O)6. What
H
30 would be the formula of:
a a triose?
Figure 2.3  Structural formula of glucose. –OH is known as a b a pentose?
hydroxyl group. There are five in glucose.

6CH2OH OH

5C OH O
H

H 4C H 1C or, more OH OH
1C O OH H simply OH

OH 3C OH
2C

H 2C OH H OH OH
HO 3C H
α-glucose

H 4C OH OH

6CH2OH

H 5C OH 5C O or, more OH O OH
6CH2OH H OH simply OH OH

glucose straight-chain form H 1C
with C atoms numbered 4C H

OH H β-glucose
OH 2C

3C OH

H

Figure 2.4  Structural formulae for the straight-chain and ring forms of glucose. Chemists often leave out the C and H atoms from
the structural formula for simplicity.

Chapter 2: Biological molecules

Roles of monosaccharides in living organisms Disaccharides and the glycosidic bond

Monosaccharides have two major functions. First, they are Disaccharides, like monosaccharides, are sugars. They
commonly used as a source of energy in respiration. This are formed by two monosaccharides joining together. The
is due to the large number of carbon–hydrogen bonds. three most common disaccharides are maltose (glucose
These bonds can be broken to release a lot of energy, which + glucose), sucrose (glucose + fructose) and lactose
is transferred to help make ATP (adenosine triphosphate) (glucose + galactose). Sucrose is the transport sugar in
from ADP (adenosine diphosphate) and phosphate. The plants and the sugar commonly bought in shops. Lactose
most important monosaccharide in energy metabolism is the sugar found in milk and is therefore an important
is glucose. constituent of the diet of young mammals.

Secondly, monosaccharides are important as building The joining of two monosaccharides takes place by a
blocks for larger molecules. For example, glucose is process known as condensation. Two examples are shown
used to make the polysaccharides starch, glycogen and in Figure 2.5. In Figure 2.5a two molecules of α-glucose
cellulose. Ribose (a pentose) is one of the molecules used combine to make the disaccharide maltose. In Figure
to make RNA (ribonucleic acid) and ATP. Deoxyribose 2.5b α-glucose and β-fructose combine to make the
(also a pentose) is one of the molecules used to make DNA disaccharide sucrose. Notice that fructose has a different
(Chapter 6). ring structure to glucose.

a monosaccharide monosaccharide disaccharide

6CH2OH O 6CH2OH O 6CH2OH 6CH2OH O
5 5 5 O5
1
4 14 1 –H2O (condensation) 4 14 2 OH 31
+H2O (hydrolysis) OH OH O OH OH
OH OH 2 OH OH OH 2 OH
3 2
33 3

OH H2O OH OH glycosidic bond
α-glucose α-glucose maltose

b monosaccharide monosaccharide disaccharide

6CH2OH OH 6CH2OH OH
5 4
5 O 1CH2OH 3 4 –H2O (condensation) O 1CH2OH 3
12 5 4 5
4 OH OH 12 6CH2OH
OH OH 2 OH OH O 6CH2OH +H2O (hydrolysis) O O
3
3 2

OH H2O OH glycosidic bond
α-glucose β-fructose sucrose

Figure 2.5  Formation of a disaccharide from two monosaccharides by condensation. a Maltose is formed from two α-glucose
molecules. This can be repeated many times to form a polysaccharide. Note that in this example the glycosidic bond is
formed between carbon atoms 1 and 4 of neighbouring glucose molecules. b Sucrose is made from an α-glucose and a
β-fructose molecule.

A monosaccharide is a molecule consisting of a single A polysaccharide is a polymer whose subunits are
sugar unit with the general formula (CH2O)n. monosaccharides joined together by glycosidic bonds.
A disaccharide is a sugar molecule consisting of two
monosaccharides joined together by a glycosidic bond.

Cambridge International AS Level Biology

For each condensation reaction, two hydroxyl (–OH) large number of possible disaccharides. The shape of the
groups line up alongside each other. One combines enzyme controlling the reaction determines which –OH
with a hydrogen atom from the other to form a water groups come alongside each other. Only a few of the
molecule. This allows an oxygen ‘bridge’ to form between possible disaccharides are common in nature.
the two molecules, holding them together and forming
a disaccharide (‘di’ means two). The bridge is called a The reverse of condensation is the addition of water,
glycosidic bond. which is known as hydrolysis (Figure 2.5). This takes place
during the digestion of disaccharides and polysaccharides,
In theory any two –OH groups can line up and, since when they are broken down to monosaccharides.
monosaccharides have many –OH groups, there are a

BOX 2.1: Testing for the presence of sugars

1 Reducing sugars – background information 2 Non-reducing sugars – background
information
The reducing sugars include all monosaccharides, such as Some disaccharides, such as sucrose, are not reducing
glucose, and some disaccharides, such as maltose.
The only common non-reducing sugar is sucrose. sugars, so you would get a negative result from Benedict’s
Reducing sugars are so called because they can carry test. In such a case, a brick-red precipitate in the test
out a type of chemical reaction known as reduction. In described below will tell you that a non-reducing sugar is
the process they are oxidised. This is made use of in the present. If both a reducing sugar and a non-reducing sugar
Benedict’s test using Benedict’s reagent. Benedict’s are present, the precipitate obtained in the test below will
reagent is copper(II) sulfate in an alkaline solution and has a be heavier than the one obtained in Benedict’s test.
distinctive blue colour. Reducing sugars reduce soluble blue In the non-reducing sugars test, the disaccharide
copper sulfate, containing copper(II) ions, to insoluble brick- is first broken down into its two monosaccharide
red copper oxide, containing copper(I). The copper oxide is constituents. The chemical reaction is hydrolysis and can
32 seen as a brick-red precipitate. be brought about by hydrochloric acid. The constituent

reducing sugar + Cu2+  → oxidised sugar + Cu+ monosaccharides will be reducing sugars and their
blue red-brown presence can be tested for using Benedict’s test after the
acid has been neutralised.
Procedure 
Procedure 
Add Benedict’s reagent to the solution you are testing
and heat it in a water bath. If a reducing sugar is present, Heat the sugar solution with hydrochloric acid. This will
the solution will gradually turn through green, yellow and release free monosaccharides. Benedict’s reagent needs
orange to red-brown as the insoluble copper(I) oxide forms alkaline conditions to work, so you need to neutralise
a precipitate. As long as you use excess Benedict’s reagent the test solution now by adding an alkali such as sodium
(more than enough to react with all of the sugar present), hydroxide. Add Benedict’s reagent and heat as before and
the intensity of the red colour is related to the concentration look for the colour change. If the solution goes red now but
of the reducing sugar. You can then estimate the didn’t in the first stage of the test, there is non-reducing
concentration using colour standards made by comparing sugar present. If there is still no colour change, then there is
the colour against the colours obtained in tests done with no sugar of any kind present.

reducing sugar solutions of known concentration. You could QUESTION
also measure the time taken for the colour to change.
Alternatively, you can use a colorimeter to measure
subtle differences in colour precisely. 2.2 a Why do you need to use excess Benedict’s
reagent if you want to get an idea of the
concentration of a sugar solution?
b Outline how you could use the Benedict’s test
to estimate the concentration of a solution of
a reducing sugar.

Chapter 2: Biological molecules

Polysaccharides O O

Polysaccharides are polymers whose subunits (monomers) 1
are monosaccharides. They are made by joining many
monosaccharide molecules by condensation. Each O1 4 O O4
successive monosaccharide is added by means of a
glycosidic bond, as in disaccharides. The final molecule O OO
may be several thousand monosaccharide units long, OO
forming a macromolecule. The most important
polysaccharides are starch, glycogen and cellulose, all Figure 2.6  Arrangement of α-glucose units in amylose. The
of which are polymers of glucose. Polysaccharides are 1,4 linkages cause the chain to turn and coil. The glycosidic
not sugars. bonds are shown in red and the hydroxyl groups are omitted.

Since glucose is the main source of energy for cells, QUESTION
it is important for living organisms to store it in an a2.3 What type of chemicalgrelyaccotsiiodnicwboounlddbbeetwineveonlved in
appropriate form. If glucose itself accumulated in cells,
it would dissolve and make the contents of the cell too the formation of glucosCeaftroommss1tarncdh6oor fgnlyecigohgebno?uring
concentrated, which would seriously affect its osmotic glucose units (1,6 link)
properties (page 82). Glucose is also a reactive molecule
and would interfere with normal cell chemistry. 1,a4 chain O Cggllauy46ctcoo5o3mssiedsui1O2cnab1itnosdn(1dr(w6ce,6boamotnefleiotdnnrwvekeae)nilgesohanfbtioounr)ing 33
These problems are avoided by converting glucose, by O OH H2O
condensation reactions, to a storage polysaccharide, which 1
is a convenient, compact, inert (unreactive) and insoluble 1,4 chain
molecule. The storage polysaccharide formed is starch 1,4 chaOin O
in plants and glycogen in animals. Glucose can be made
available again quickly by an enzyme-controlled reaction. 1,4 chain 6 removal of
b O 5 O6CH2OwHater
Starch and glycogen 14 1 (condensation)
25 O
Starch is a mixture of two substances – amylose and O3 4 OH 1
amylopectin. Amylose is made by condensations between H2O
α-glucose molecules, as shown in Figure 2.5a. In this way,
a long, unbranching chain of several thousand 1,4 linked O 32 O
glucose molecules is built up. (‘1,4 linked’ means they
are linked between carbon atoms 1 and 4 of successive 6CH2OH
glucose units.) The chains are curved (Figure 2.6) and
coil up into helical structures like springs, making the 5 O
final molecule more compact. Amylopectin is also made 4
of many 1,4 linked α-glucose molecules, but the chains 1
are shorter than in amylose, and branch out to the sides. O3
The branches are formed by 1,6 linkages, as shown in 2O
Figure 2.7.
1,4 links
Mixtures of amylose and amylopectin molecules build
up into relatively large starch grains, which are commonly 1,6 link
found in chloroplasts and in storage organs such as potato
tubers and the seeds of cereals and legumes (Figure 2.8). b 1,4 links
Starch grains are easily seen with a light microscope,
especially if stained; rubbing a freshly cut potato tuber 1,4 links 1,6 link
on a glass slide and staining with iodine–potassium
iodide solution (Box 2.2) is a quick method of preparing a Figure 2.7  Branching structure of amylopectin and glycogen.
specimen for viewing. a Formation o1f,a4 1lin,6kslink, a branchpoint, b Overall structure
of an amylopectin or glycogen molecule. Amylopectin and
Starch is never found in animal cells. Instead, a glycogen only differ in the amount of branching of their
substance with molecules very like those of amylopectin is glucose chains.

Cambridge International AS Level Biology

used as the storage carbohydrate. This is called glycogen. Cellulose
Glycogen, like amylopectin, is made of chains of
1,4 linked α-glucose with 1,6 linkages forming branches Cellulose is the most abundant organic molecule on
(Figure 2.7b). Glycogen molecules tend to be even the planet, due to its presence in plant cell walls and
more branched than amylopectin molecules. Glycogen its slow rate of breakdown in nature. It has a structural
molecules clump together to form granules, which are role, being a mechanically strong molecule, unlike starch
visible in liver cells and muscle cells, where they form an and glycogen. However, the only difference between
energy reserve. cellulose and starch and glycogen is that cellulose is a
polymer of β-glucose, not α-glucose.
Remember that in the β-isomer, the –OH group on
QUESTION carbon atom 1 projects above the ring (Figure 2.4 on

2.4 List five ways in which the molecular structures of page 30). In order to form a glycosidic bond with carbon
glycogen and amylopectin are similar. atom 4, where the –OH group is below the ring, one
glucose molecule must be upside down (rotated 180°)
relative to the other. Thus successive glucose units are
linked at 180° to each other, as shown in Figure 2.9.
This arrangement of β-glucose molecules results in
a strong molecule because the hydrogen atoms of –OH
groups are weakly attracted to oxygen atoms in the same
cellulose molecule (the oxygen of the glucose ring) and
also to oxygen atoms of –OH groups in neighbouring
molecules. These hydrogen bonds (page 35) are
individually weak, but so many can form, due to the
large number of –OH groups, that collectively they
34 provide enormous strength. Between 60 and 70 cellulose
molecules become tightly cross-linked to form bundles
called microfibrils. Microfibrils are in turn held together
in bundles called fibres by hydrogen bonding.

Figure 2.8  False-colour scanning electron micrograph of a a OH groups lined up to β-glucose
slice through a raw potato showing cells containing starch form a glycosidic bond 2 rotated
grains or starch-containing organelles (coloured red) (× 260). 6
5 O OH OH 3 180°
BOX 2.2: Testing for the presence of starch 14 1
Background information 4
Starch molecules tend to curl up into long spirals. The
hole that runs down the middle of this spiral is just the OH 3 2 5 OH
right size for iodine molecules to fit into. To test for starch, 6 O
you use something called ‘iodine solution’. (In fact, iodine β-glucose (only the relevant
won’t dissolve in water, so the ‘iodine solution’ is actually –OH groups are shown) OO OO
iodine in potassium iodide solution.) The starch–iodine
complex that forms has a strong blue-black colour. b
Procedure  OO
Iodine solution is orange-brown. Add a drop of iodine
solution to the solid or liquid substance to be tested. O OO OO
A blue-black colour is quickly produced if starch
is present. Figure 2.9  a Two β-glucose molecules lined up to form a
1,4 link. Note that one glucose molecule must be rotated
180° relative to the other, b Arrangement of β-glucose units
in cellulose: glycosidic bonds are shown in red and hydroxyl
groups are omitted.

Chapter 2: Biological molecules

A cell wall typically has several layers of fibres, running Dipoles and hydrogen bonds
in different directions to increase strength (Figure 2.10).
Cellulose makes up about 20–40% of the average cell wall; When atoms in molecules are held together by covalent
other molecules help to cross-link the cellulose fibres, and bonds, they share electrons with each other. Each shared
some form a glue-like matrix around the fibres, which pair of electrons forms one covalent bond. For example, in
further increases strength. a water molecule, two hydrogen atoms each share a pair of
electrons with an oxygen atom, forming a molecule with
Cellulose fibres have a very high tensile strength, the formula H2O.
almost equal to that of steel. This means that if pulled at
both ends they are very difficult to stretch or break, and oxygen atom
makes it possible for a cell to withstand the large pressures O covalent bond
that develop within it as a result of osmosis (page 82). H H hydrogen atom
Without the wall, the cell would burst when in a dilute
solution. These pressures help provide support for the However, the electrons are not shared absolutely
plant by making tissues rigid, and are responsible for equally. In water, the oxygen atom gets slightly more than
cell expansion during growth. The arrangement of fibres its fair share, and so has a small negative charge, written
around the cell helps to determine the shape of the cell as δ− (delta minus). The hydrogen atoms get slightly less
it grows. than their fair share, and so have a small positive charge,
written δ+ (delta plus).
Despite their strength, cellulose fibres are freely
permeable, allowing water and solutes to reach or leave This unequal distribution of charge is called a dipole.
the cell surface membrane.
δ+H Oδ−Hδ+
QUESTION
2.5 Make a table to show three ways in which the In water, the negatively charged oxygen of one 35
molecule is attracted to a positively charged hydrogen of
molecular structures of amylose and cellulose differ. another, and this attraction is called a hydrogen bond (see
diagram below). It is much weaker than a covalent bond,
but still has a very significant effect. You will find out how
hydrogen bonds affect the properties of water on pages
46–47.

δ+H O
H

H hydrogen bond
O δ−

H

cell wall cellulose bre micro bril
(50nm diameter) (10nm diameter)
made of many made of 60–70
micro brils molecules

glycosidic bond

glucose ring structure – part of one hydrogen bond
cellulose molecule

Figure 2.10  Structure of cellulose.

Cambridge International AS Level Biology

Dipoles occur in many different molecules, particularly Lipids
wherever there is an –OH, –CO or –NH group. Hydrogen
bonds can form between these groups, because the It is difficult to define precisely what we mean by a ‘lipid’
negatively charged part of one group is attracted to the because lipids are a very varied group of chemicals. They
positively charged part of another. These bonds are very are all organic molecules which are insoluble in water.
important in the structure and properties of carbohydrates The most familiar lipids are fats and oils. Fats are solid at
and proteins. room temperature and oils are liquid at room temperature
– chemically they are very similar. We could say that true
C Oδ− δ+H N lipids are esters formed by fatty acids combining with
an alcohol.
Molecules which have groups with dipoles, such as
sugars, are said to be polar. They are attracted to water Fatty acids
molecules, because the water molecules also have dipoles.
Such molecules are said to be hydrophilic (water-loving), Fatty acids are a series of acids, some of which are found
and they tend to be soluble in water. Molecules which in fats (lipids). They contain the acidic group –COOH,
do not have dipoles are said to be non-polar. They are known as a carboxyl group. The larger molecules in the
not attracted to water, and they are hydrophobic (water- series have long hydrocarbon tails attached to the acid
hating). Such properties make possible the formation of ‘head’ of the molecule (Figure 2.11). As the name suggests,
cell membranes (Chapter 4). the hydrocarbon tails consist of a chain of carbon atoms
combined with hydrogen. The chain is often 15 or 17
carbon atoms long.

36 OH O acid head OH O
C C

HC H HC H

HCH hydrophobic HCH
HC H hydrocarbon tail HC H

HCH HCH

HC H HC H
HCH HCH

HC H HC H
HCH
C H double bond
HC H causes kink

HCH C H in tail

HC H HCH
HCH
CH
C
HH CH
HCH
H
CH

CH

saturated fatty acid HCH

HCH

H unsaturated fatty acid

Figure 2.11  Structure of a saturated and an unsaturated fatty acidu.nPshatoutroagteradpfahtstyofacmidodels are shown to the sides of the
structures. In the models, hysadtruorgaetendisfawtthyiateci,dcarbon is grey and oxygen is red.

Chapter 2: Biological molecules

The tails of some fatty acids have double bonds between C COOH + HO C C COOC + H2O
neighbouring carbon atoms, like this: –C   C–. Such fatty
acids are described as unsaturated because they do not acid alcohol ester
contain the maximum possible amount of hydrogen. They
form unsaturated lipids. Double bonds make fatty acids The –COOH group on the acid reacts with the –OH
and lipids melt more easily – for example, most oils are group on the alcohol to form the ester bond , –COO− .
unsaturated. If there is more than one double bond, the This is a condensation reaction because water is formed
fatty acid or lipid is described as polyunsaturated; if there as a product. The resulting ester can be converted back to
is only one it is monounsaturated. acid and alcohol by the reverse reaction of adding water, a
reaction known as hydrolysis.
Animal lipids are often saturated (no double
bonds) and occur as fats, whereas plant lipids are often Triglycerides
unsaturated and occur as oils, such as olive oil and
sunflower oil. The most common lipids are triglycerides (Figure 2.13).
These are fats and oils. A glyceride is an ester formed by
Alcohols and esters a fatty acid combining with the alcohol glycerol. As we
have seen, glycerol has three hydroxyl groups. Each one is
Alcohols are a series of organic molecules which contain a able to undergo a condensation reaction with a fatty acid.
hydroxyl group, –OH, attached to a carbon atom. Glycerol When a triglyceride is made, as shown in Figure 2.12, the
is an alcohol with three hydroxyl groups (Figure 2.12). final molecule contains three fatty acids tails and three
ester bonds (‘tri’ means three). The tails can vary in length,
The reaction between an acid and an alcohol produces depending on the fatty acids used.
a chemical known as an ester. The chemical link between
the acid and the alcohol is known as an ester bond or an
ester linkage.

37

HO head 3 hydrocarbon
tails
H
O

H C OH HO C HCOC
O
condensation O
H C OH HO C
O HCOC

H C OH HO C 3H2O O

HCOC

H + 3 fatty acid molecules H
with hydrocarbon tails
glycerol triglyceride
molecule

fatty acid fatty acid

glycerol
glycerol
or, more simply fatty acid condensation fatty acid

fatty acid 3H2O fatty acid

Key fatty acid ester bond
glycerol

Figure 2.12  Formation of a triglyceride from glycerol and three fatty acid molecules.

Cambridge International AS Level Biology

Triglycerides are insoluble in water but are soluble in Phospholipids
certain organic solvents, including ether, chloroform and
ethanol. This is because of the non-polar nature of the Phospholipids are a special type of lipid. Each molecule
hydrocarbon tails: they have no uneven distribution of has the unusual property of having one end which is
electrical charge. Consequently, they will not mix freely soluble in water. This is because one of the three fatty
with water molecules and are described as hydrophobic acid molecules is replaced by a phosphate group, which is
(water-hating). Figure 2.13 shows a simplified diagram of a polar (page 35) and can therefore dissolve in water. The
triglyceride. phosphate group is hydrophilic (water-loving) and makes
the head of a phospholipid molecule hydrophilic, although
three hydrophobic fatty acid tails the two remaining tails are still hydrophobic (Figure 2.15).
This allows the molecules to form a membrane around a
glycerol cell, where the hydrophilc heads lie in the watery solutions
Figure 2.13  Diagrammatic representation of a triglyceride on the outside of the membrane, and the hydrophobic tails
molecule. form a layer that is impermeable to hydrophilic substances.
The biological significance of this will become apparent
when we study membrane structure (Chapter 4).

Roles of triglycerides hydrophilic head two hydrophobic
containing fatty acid tails
Lipids make excellent energy reserves because they phosphate group
are even richer in carbon–hydrogen bonds than
carbohydrates. A given mass of lipid will therefore
38 yield more energy on oxidation than the same mass of Figure 2.15  Diagrammatic representation of a phospholipid
carbohydrate (it has a higher calorific value), an important molecule. Compare with Figure 2.13.

advantage for a storage product.
Fat is stored in a number of places in the human
body, particularly just below the dermis of the skin and BOX 2.3: Testing for the presence of lipids

around the kidneys. Below the skin it also acts as an Background information
insulator against loss of heat. Blubber, a lipid found in
Lipids are insoluble in water, but soluble in ethanol
(alcohol). This fact is made use of in the emulsion test
sea mammals like whales, has a similar function, as well for lipids.
as providing buoyancy. An unusual role for lipids is as a
metabolic source of water. When oxidised in respiration Procedure 
they are converted to carbon dioxide and water. The
The substance that is thought to contain lipids is shaken
vigorously with some absolute ethanol (ethanol with little
water may be of importance in very dry habitats. For or no water in it). This allows any lipids in the substance
example, the desert kangaroo rat (Figure 2.14) never to dissolve in the ethanol. The ethanol is then poured into
drinks water and survives on metabolic water from its a tube containing water. If lipid is present, a cloudy white
fat intake. suspension is formed.

Further information

If there is no lipid present, the ethanol just mixes into the
water. Light can pass straight through this mixture,
so it looks completely transparent. But if there is lipid
dissolved in the ethanol, it cannot remain dissolved
when mixed with the water. The lipid molecules form tiny
droplets throughout the liquid. This kind of mixture is
called an emulsion. The droplets reflect and scatter light,
making the liquid look white and cloudy.

Figure 2.14  The desert kangaroo rat uses metabolism of food
to provide most of the water it needs.

Chapter 2: Biological molecules

Proteins a

Proteins are an extremely important class of H R O This group varies in
macromolecule in living organisms. More than 50% of N C C di erent amino acids.
the dry mass of most cells is protein. Proteins have many H It is known as the R group
important functions. For example: H OH or side-chain.

■■ all enzymes are proteins amine group carboxylic
■■ proteins are essential components of cell membranes – acid group

their functions in membranes, such as receptor b
proteins and signalling proteins, are discussed in H
Chapter 4
■■ some hormones are proteins – for example, insulin and HO
glucagon NC C
■■ the oxygen-carrying pigments haemoglobin and
myoglobin are proteins H OH
■■ antibodies, which attack and destroy invading H
microorganisms, are proteins
■■ collagen, another protein, adds strength to many glycine
animal tissues, such as bone and the walls of arteries
■■ hair, nails and the surface layers of skin contain the Figure 2.16  a The general structure of an amino acid.
protein keratin b Structure of the simplest amino acid, glycine, in which the R
■■ actin and myosin are the proteins responsible for group is H, hydrogen. R groups for the 20 naturally occurring
muscle contraction amino acids are shown in Appendix 1.
■■ proteins may be storage products – for example, casein
in milk and ovalbumin in egg white. The only way in which amino acids differ from each 39
other is in the remaining, fourth, group of atoms bonded
Despite their tremendous range of functions, all proteins to the central carbon. This is called the R group. There are
are made from the same basic monomers. These are amino 20 different amino acids which occur in the proteins of
acids. living organisms, all with a different R group. You can see
their molecular formulae in Appendix 1. (You do not need
Amino acids to remember all the different R groups.) Appendix 1 also
Figure 2.16 shows the general structure of all amino acids shows the three-letter abbreviations commonly used by
and of glycine, the simplest amino acid. They all have a scientists for the names of the amino acids. Many other
central carbon atom which is bonded to an amine amino acids have been synthesised in laboratories.
tghroesuept,w–oNgHr2o,uapnsdwahcicahrbgoixveylaicmaicniod group, –COOH. It is
acids their name. The The peptide bond
third component that is always bonded to the carbon atom
is a hydrogen atom. Figure 2.17 shows how two amino acids can join together.
One loses a hydroxyl (–OH) group from its carboxylic
acid group, while the other loses a hydrogen atom from
its amine group. This leaves a carbon atom of the first
amino acid free to bond with the nitrogen atom of the
second. The link is called a peptide bond. The oxygen
and two hydrogen atoms removed from the amino acids

amino acid amino acid dipeptide

RR RO R
H O H O –H2O (condensation) H
NC C NC C NC CNC O
H OH H H OH +H2O (hydrolysis) H H C
H
OH

HH

H2O peptide bond

Figure 2.17  Amino acids link together by the loss of a molecule of water to form a peptide bond.

Cambridge International AS Level Biology

form a water molecule. We have seen this type of reaction, Primary structure
a condensation reaction, in the formation of glycosidic
bonds (Figure 2.5 on page 31) and in the synthesis of A polypeptide or protein molecule may contain several
triglycerides (Figure 2.12 on page 37). hundred amino acids linked into a long chain. The
particular amino acids contained in the chain, and
The new molecule which has been formed, made up the sequence in which they are joined, is called the
of two linked amino acids, is called a dipeptide. Any primary structure of the protein. Figure 2.18 shows the
number of extra amino acids could be added to the chain primary structure of the protein ribonuclease, an enzyme.
in a series of condensation reactions. A molecule made up
of many amino acids linked together by peptide bonds is There are an enormous number of different possible
called a polypeptide. A polypeptide is another example primary structures. Even a change in one amino acid in
of a polymer and a macromolecule, like a polysaccharide. a chain made up of thousands may completely alter the
A complete protein molecule may contain just one properties of the polypeptide or protein.
polypeptide chain, or it may have two or more chains
which interact with each other. Secondary structure
The amino acids in a polypeptide chain have an effect
In living cells, ribosomes are the sites where amino on each other even if they are not directly next to each
acids are joined together to form polypeptides. The
reaction is controlled by enzymes. You can read more other. A polypeptide chain, or part of it, often coils into
about this on pages 119–121. a corkscrew shape called an α-helix (Figure 2.19a). This
secondary structure is due to hydrogen bonding between
Polypeptides can be broken down to amino acids by the oxygen of the –CO– group of one amino acid and
breaking the peptide bonds. This is a hydrolysis reaction,
involving the addition of water (Figure 2.17), and happens the hydrogen of the –NH– group of the amino acid four
places ahead of it. Each amino acid has an –NH– and a
naturally in the stomach and small intestine during –CO– group, and Figure 2.19a shows that all these groups
digestion. Here, protein molecules in food are hydrolysed
40 into amino acids before being absorbed into the blood. are involved in hydrogen bonding in the α-helix, holding
the structure firmly in shape. Hydrogen bonding is a
result of the polar characteristics of the –CO– and –NH–
groups (page 36).
Sometimes hydrogen bonding can result in a much
looser, straighter shape than the α-helix, which is called a

Ala Lys Phe Glu Arg Gln His Met
10 Asp
Ala Ala

Thr Ser
1 Glu
Lys Ser Ser 20 Ala Ser Ser
Ala Thr
+H3N Asn Ser

30 Tyr 80
Lys Met Met IIe Ser Met Thr Ser Tyr Ser Gln Tyr
Ser Gln Asn Cys Asp Thr Cys
Cys
Arg Asn
Asn Ser Gly Arg 70 Thr Lys Cys
Leu Ser Ala
Lys 90 Thr Glu Gln Asn
Val Pro Val Tyr Pro Asn Gly Gly Val
Ser Ala 120 Asn
Val
Thr Tyr 124 Asp Phe His

Lys Pro CO 110 Glu Lys
Asp Asn
Cys O– Ala Cys Ser Gln
Arg Ala Tyr Val 60
40 Cys Cys
Lys Lys 100 IIe IIe Val
Thr Gln His
Thr Ala Asn Lys Ala
Pro Gln
Val
Val Asn Thr Phe Val 50 Asp
Ser Ala
His Glu Leu

Figure 2.18  The primary structure of ribonuclease. Ribonuclease is an enzyme found in pancreatic juice, which hydrolyses
(digests) RNA (Chapter 6). Notice that at one end of the amino acid chain tNhearnedisCatner–mNiHn3a+lsg,rroeuspp,ewcthivileelay.tNthoeteotthheeruesnedofththerreeeis-
a –COO− group. These are known as the amino and carboxyl ends, or the
letter abbreviations for the amino acids. These are explained in Appendix 1.