Cambridge International AS and A Level Biology: Coursebook (third edition)

Mary Jones, Richard Fosbery, Jennifer Gregory and Dennis Taylor

Cambridge International AS and A Level

BiologyCoursebook

Third edition

CAMBRIDGE UNIVERSITY PRESSCambridge, New York, Melbourne, Madrid, Cape Town, Singapore, São Paulo, Delhi, Mexico City

Cambridge University Press1 e Edinburgh Building, Cambridge CB2 8RU, UK

www.cambridge.orgInformation on this title: www.cambridge.org/9781107609211

© Cambridge University Press 2003, 2013

1 is publication is in copyright. Subject to statutory exceptionand to the provisions of relevant collective licensing agreements, no reproduction of any part may take place without the written permission of Cambridge University Press.

First published 2003Second edition 2007

ird edition 2013

Printed in the United Kingdom by Latimer Trend

A catalogue record for this publication is available from the British Library

ISBN 978-1-107-60921-1 Paperback with CD-ROM for Windows® and Mac®

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1Reprinted 2013

iiiContents

Contents

6 Genetic control !"#The structure of DNA and RNA !"#DNA replication !"$Genes and mutations !"%DNA, RNA and protein synthesis !"%End-of-chapter questions !!$

7 Transport in multicellular plants !!&The need for transport systems in multicellular organisms !!&The transport of water !'"Transport in multicellular plants !'"Translocation !##Di( erences between sieve tubes and xylem vessels !#)End-of-chapter questions !#&

8 The mammalian transport system !**The mammalian cardiovascular system !**Blood plasma and tissue + uid !$"Lymph !$"Blood !$!Haemoglobin !$*Problems with oxygen transport !$)End-of-chapter questions !,"

9 The mammalian heart !,*The cardiac cycle !,,Control of the heart beat !,&End-of-chapter questions !)"

10 Gas exchange !)*Lungs !)*Trachea, bronchi and bronchioles !)*Alveoli !))End-of-chapter questions !)&

11 Smoking !&'Tobacco smoke !&'Lung diseases !&'Cardiovascular diseases !&$Proving the links between smoking and lung disease !&&Prevention and cure of coronary heart disease !%'End-of-chapter questions !%*

Introduction vi

1 Cell structure !Why cells? 'Cell biology and microscopy 'Animal and plant cells have features in common *Di( erences between animal and plant cells $Units of measurement in cell studies ,Electron microscopes &Ultrastructure of an animal cell !#Structures and functions of organelles !#Ultrastructure of a plant cell !&Two fundamentally di( erent types of cell !&Tissues and organs '"End-of-chapter questions '*

2 Biological molecules '%The building blocks of life #"Monomers, polymers and macromolecules #"Carbohydrates #"Lipids #)Proteins #%Water *)End-of-chapter questions *%

3 Enzymes $*Enzymes reduce activation energy $)The course of a reaction $)Enzyme inhibitors ,'End-of-chapter questions ,#

4 Cell membranes and transport ,%Phospholipids ,%Structure of membranes )"Transport across the cell surface membrane )#End-of-chapter questions &!

5 Cell and nuclear division &,The nucleus contains chromosomes &,The structure of chromosomes &&Two types of nuclear division &%Mitosis in an animal cell %"Cancer %#End-of-chapter questions %%

iv

12 Infectious diseases !%)Worldwide importance of infectious diseases !%)Cholera !%&Malaria '""Acquired immune de- ciency syndrome (AIDS) '"#Tuberculosis (TB) '"&Antibiotics '!!End-of-chapter questions '!#

13 Immunity '!)Defence against disease '!)Cells of the immune system '!&Active and passive immunity ''$Vaccination '',Problems with vaccines '')The eradication of smallpox ''&Measles '#"End-of-chapter questions '#!

14 Ecology '#$Energy + ow through organisms and ecosystems '#,Matter recycling in ecosystems '*!The nitrogen cycle '*!End-of-chapter questions '*$

15 Advanced practical skills '*&Experiments '*&Variables and making measurements '*%Estimating uncertainty in measurement '$)Recording quantitative results '$&Constructing a line graph '$%Constructing bar charts and histograms ',"Drawing conclusions ',!Describing data ',!Making calculations from data ',!Explaining your results ',#Identifying sources of error and suggesting improvements ',#Drawings ',*End-of-chapter questions ',$

16 Energy and respiration ',&The need for energy in living organisms ',&Work ',&ATP ')"Respiration ')#Anaerobic respiration ')%Respiratory substrates '&"End-of-chapter questions '&#

17 Photosynthesis '&)An energy transfer process '&)The light-dependent reactions of photosynthesis '&&The light-independent reactions of photosynthesis '%"Leaf structure and function '%"Chloroplast structure and function '%#Factors necessary for photosynthesis '%*Trapping light energy '%$End-of-chapter questions '%)

18 Regulation and control #"!Homeostasis #"'Excretion #"'The structure of the kidney #"#Control of water content #!!Nervous communication #!*Hormonal communication #'%Plant growth regulators ##,Electrical communication in plants ##%End-of-chapter questions #*"

19 Inherited change #*)Meiosis #*)Genetics #*&Genotype a( ects phenotype #$!Inheriting genes #$'Multiple alleles #$*Sex inheritance #$$Sex linkage #$$Dihybrid crosses #$)The F2 (chi-squared) test #$%Mutations #,!Environment and phenotype #,#End-of-chapter questions #,#

20 Selection and evolution #,)Natural selection #,&Evolution #)"The Darwin–Wallace theory of evolution by natural selection #)*Species and speciation #)$Arti- cial selection #))End-of-chapter questions #)&

21 Biodiversity and conservation #&'The - ve-kingdom classi- cation #&'Maintaining biodiversity #&$Endangered species #&$End-of-chapter questions #%'

Contents

vContents

22 Gene technology #%$Gene technology #%$Bene- ts of gene technology #%%Potential hazards of gene technology *""Social and ethical implications of genetic engineering *"'Electrophoresis *"#Cystic - brosis *"*The genetic counsellor *")Genetic screening *"%End-of-chapter questions *!!

23 Biotechnology *!*Mining with microorganisms *!*Large-scale production techniques *!,Advantages of batch and continuous culture *!%How penicillin works *'"Immobilising enzymes *''Monoclonal antibodies *'*End-of-chapter questions *')

24 Crop plants *#!Cereal crops *#!Maize *##C4 plants *#*Adaptations for di. cult environments *#)Crop improvement **"End-of-chapter questions **)

25 Aspects of human reproduction *$!Gametogenesis *$#Human menstrual cycle *$,Birth control *$)Infertility *$%End-of-chapter questions *,*

26 Planning, analysis and evaluation *,&Planning an investigation *,&Analysis, conclusions and evaluation *)#End-of-chapter questions *&"

Appendix 1 Amino acid R groups *&*

Appendix 2 DNA triplet codes *&$

Glossary *&,

Index $"!

Acknowledgements $!"

CD-ROM Advice on how to revise for and approach examinations

Chapter summaries

Multiple choice tests for Chapters !–!*

Answers to self-assessment questions

Answers to end-of-chapter questions

vi Introduction

Introduction

1 is new edition is fully updated for the 2014 syllabus to help you do well in your Cambridge International Examinations AS and A level Biology (9700) courses. 1 e book and its accompanying CD-ROM provide a self-contained resource for studying these courses, with improved focus on exam preparation.

• Chapters 1–15 provide complete coverage of the AS level syllabus. 1 is is also the 3 rst year of study for A level. 1 e AS syllabus is designed for students with O level or IGCSE Biology.

• Chapters 16–26 cover all the material for the second year of study for A level. 1 is includes the relevant Core material and the Applications of Biology section.

Extension material is clearly marked with the following symbol E and a dotted line runs down alongside the text to mark this additional content.

Important features of this new edition include the following.1 e sequence of chapters mirrors the sequence of topics

in the syllabus, which makes it easy to navigate. (Your teacher may, however, tackle subjects in a di4 erent order.) Syllabus sections G and H are split into three and two chapters respectively for additional convenience (see table).

Level Syllabus section ChapterAS levelCore syllabus

A Cell structure 1

B Biological molecules 2C Enzymes 3D Cell membranes and transport 4E Cell and nuclear division 5F Genetic control 6G Transport Transport in multicellular plants ! e mammalian transport system ! e mammalian heart

789

H Gas exchange and smoking Gas exchange Smoking

1011

I Infectious disease 12J Immunity 13K Ecology 14 Advanced practical skills 15

A level L Energy and respiration 16M Photosynthesis 17N Regulation and control 18O Inherited change 19

Level Syllabus section ChapterP Selection and evolution 20

Applications of Biology

Q Biodiversity and conservation

21

R Gene technology 22S Biotechnology 23T Crop plants 24U Aspects of human reproduction 25 Planning, analysis and evaluation 26

1 ere are two new chapters covering practical skills: Chapter 15 (AS level) and Chapter 26 (A level). Interesting information that is not required by the syllabus but will aid understanding, is marked as ‘extension material’ by orange dotted bars.

Each chapter contains self-assessment questions (SAQs). 1 ese are to help you think about, understand and remember what you have just read. Each chapter ends with a set of chapter-related questions, ranging from formative questions (requiring simple recall or reference to the text) to more challenging structured or essay questions requiring understanding as well as the other skills tested in examinations. Some of the questions are past Cambridge examination questions so you can familiarise yourself with the style of the examination questions.

Biology involves many technical terms. Each time a new term is introduced, it is shown in bold orange and its meaning explained. 1 e glossary contains de3 nitions of the key terms used in the book.

At the end of your course, you will be tested on three sets of Assessment Objectives.

• Knowledge with understanding. You are expected to know and understand all the facts and concepts listed in the syllabus. 1 ese are all covered in this book.

• Handling information and solving problems. Questions testing these skills expect you to use your knowledge and understanding in an unfamiliar context. A good knowledge and understanding of this book will enable you to approach new situations with con3 dence.

• Experimental skills and investigations. 1 is involves practical work. An examination will test your practical skills so try to do plenty of practical work. Key information is provided on some practical aspects of the course in Chapters 15 and 26.

Additional help and guidance are available on the accompanying CD-ROM.

11 Cell structure

In the early days of microscopy an English scientist, Robert Hooke, decided to examine thin slices of plant 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 1.1.

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. " e 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.

the chloroplasts, cell wall, large permanent vacuole, tonoplast and plasmodesmata of plant cells

outline the functions of the structures listed above

compare the structure of typical animal and plant cells

calculate the linear magni! cation of, and the actual sizes of, specimens from drawings and photographs

describe the structure of a prokaryotic cell, and compare and contrast the structure of prokaryotic cells with that of eukaryotic cells

explain how eukaryotic cells may be organised into tissues and organs, with reference to transverse sections of stems, roots and leaves

draw and label low-power plan diagrams of tissues and organs.

By the end of this chapter you should be able to:

describe and interpret drawings and photographs of typical animal and plant cells as seen using the light microscope and make microscopical measurements using an eyepiece graticule and stage micrometer

be familiar with the units used in cell studies

explain the meanings of, and distinguish between, the terms resolution and magni! cation

describe and interpret drawings and photographs of typical animal and plant cells as seen using the electron microscope, recognising rough and smooth endoplasmic reticulum (ER), Golgi apparatus, mitochondria, ribosomes, lysosomes, cell surface membrane, centrioles, nucleus (including the nuclear envelope and nucleolus) and microvilli, as well as

1 Cell structure

Figure 1.1 Drawing of cork cells published by Robert Hooke in 1665.

22 1 Cell structure

Why cells?A cell can be thought of as a bag in which the chemistry of life is allowed to occur, partially separated from the environment outside the cell. " e thin membrane which surrounds all cells is essential in controlling exchange between the cell and its environment. It is a very e# ective barrier, but also allows a controlled tra$ c of materials across it in both directions. " e membrane is therefore described as partially permeable. If it were freely permeable, life could not exist, because the chemicals of the cell would simply mix with the surrounding chemicals by di# usion, (page 73).

Cell biology and microscopy" e study of cells has given rise to an important branch of biology known as cell biology. Cells can now be studied by many di# erent methods, but scientists began simply by looking at them, using various types of microscope.

" ere are two fundamentally di# erent types of microscope now in use: the light microscope and the electron microscope. Both use a form of radiation in order to create an image of the specimen being examined. " e light microscope uses light as a source of radiation, while the electron microscope uses electrons, for reasons which are discussed later.

Light microscopy" e ‘golden age’ of light microscopy could be said to be the 19th century. Microscopes had been available since the beginning of the 17th century but, when dramatic improvements were made in the quality of glass lenses in the early 19th century, interest among scientists became widespread. " e fascination of the microscopic world that opened up in biology inspired rapid progress both in microscope design and, equally importantly, in preparing material for examination with microscopes. " is branch of biology is known as cytology. Figure 1.2 shows how the light microscope works.

By 1900, all the structures shown in Figures 1.3, 1.4 and 1.5, except lysosomes, had been discovered. Figure 1.3 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 1.2 How the light microscope works.

eyepiece

light beam

objective

glass slide

condenser

iris diaphragm

light source Condenser iris diaphragm is closed slightly to produce a narrow beam of light.

Condenser lens focuses the light onto the specimen held between the cover slip and slide.

Objective lens collects light passing through the specimen and produces a magni!ed image.

Eyepiece lens magni!es and focuses the image from the objective onto the eye.

pathway of light

cover slip

Figure 1.3 Structure of a generalised animal cell (diameter about 20 Pm) as seen with a very high quality light microscope.

Golgi apparatus

cytoplasm

mitochondria

small structures thatare di#cult to identify

cell surface membrane

centriole – always found near nucleus,has a role in nuclear division

nuclear envelope

chromatin –deeply stainingand thread-like nucleus

nucleolus –deeply staining

31 Cell structure

SAQ 1.1

Using Figures 1.3 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.

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

Golgi apparatus

cytoplasm

chromatin –deeply stainingand thread-like

nucleus small structures thatare di#cult to identify

nucleolus –deeply staining

nuclear envelope

mitochondria

chloroplast

grana just visible

tonoplast – membranesurrounding vacuole

vacuole – largewith central position

plasmodesma –connects cytoplasmof neighbouring cells

cell wall

cell wall ofneighbouringcell

cell surface membrane(pressed against cell wall)

middle lamella – thin layer holding cells together, contains calcium pectate

Figure 1.4 Cells from the lining of the human cheek (u 500), each showing a centrally placed nucleus which is a typical animal cell characteristic. The cells are part of a tissue known as squamous ($ attened) epithelium.

Figure 1.4 shows some actual human cells and Figure 1.6 shows an actual plant cell taken from a leaf.

Figure 1.6 Photomicrograph of a cell in a moss leaf (u1400).

44 1 Cell structure

Box 1A Biological drawing

You need the following equipment:

• pencil (HB)• pencil sharpener• eraser• ruler• plain paper.

Here are some guidelines for the quality of your drawing:

• always use a pencil, not a pen• don’t use shading• use clear, continuous lines• use accurate proportions and observation – not a

textbook version.

For a low-power drawing (see Figure 1.7):

• don’t draw individual cells• draw all tissues completely enclosed by lines• draw a correct interpretation of the distribution of

tissues• a representative portion may be drawn (e.g. half a

transverse section).

For a high-power drawing:

• draw only a few representative cells• draw the cell wall of all plant cells• don’t draw the nucleus as a solid blob.

Some guidelines for the quality of your labelling:

• label all tissues and relevant structures• identify parts correctly• use a ruler for label lines

Figure 1.7 The right side of this low-power drawing shows examples of good technique, while the left side shows many of the pitfalls you should avoid.

• arrange label lines neatly and ensure they don’t cross over each other

• annotate your drawing if necessary (i.e. provide short notes with one or more of the labels in order to describe or explain features of biological interest)

• add a scale line at the bottom of the drawing if appropriate

• use a pencil, not a pen.

An example of a drawing of a section through the stem of Helianthus is shown below. Biological drawing is also covered in Chapter 15, page 264.

Animal and plant cells have features in commonIn animals and plants each cell is surrounded by a very thin cell surface membrane, which is too thin to be seen with a light microscope. " is is also sometimes referred to as the plasma membrane.

Many of the cell contents are colourless and transparent so they need to be stained to be seen. Each cell has a nucleus, which is a relatively large structure that stains intensely and is therefore very conspicuous. " e deeply staining material in the nucleus is called chromatin and is a mass of loosely coiled threads. " is material collects together to form visible separate chromosomes during nuclear division

51 Cell structure

(see page 86). It contains DNA (deoxyribonucleic acid), a molecule which contains the instructions that control the activities of the cell (see Chapter 6). Within the nucleus an even more deeply staining area is visible, the nucleolus, which is made of loops of DNA from several chromosomes. " e number of nucleoli is variable, one to % ve being common in mammals.

" e material between the nucleus and the cell surface membrane is known as cytoplasm. Cytoplasm is an aqueous (watery) material, varying from a & uid to a jelly-like consistency. Many small structures can be seen within it. " ese have been likened to small organs and hence are known as organelles. An organelle can be de% ned as a functionally and structurally distinct part of a cell. Organelles themselves are often surrounded by membranes so that their activities can be separated from the surrounding cytoplasm. " is is described as compartmentalisation. Having separate compartments is essential for a structure as complex as an animal or plant cell to work e$ ciently. Since each type of organelle has its own function, the cell is said to show division of labour, a sharing of the work between di# erent specialised organelles.

" e most numerous organelles seen with the light microscope are usually mitochondria (singular: mitochondrion). Mitochondria are only just visible, but % lms of living cells, taken with the aid of a light microscope, have shown that they can move about, change shape and divide. " ey are specialised to carry out aerobic respiration.

" e use of special stains containing silver enabled the Golgi apparatus to be detected for the % rst time in 1898 by Camillo Golgi. " e Golgi apparatus is part of a complex internal sorting and distribution system within the cell (see page 16). It is also sometimes called the Golgi body or Golgi complex.

Di! erences between animal and plant cells" e only structure commonly found in animal cells which is absent from plant cells is the centriole. Plant cells also di# er from animal cells in possessing cell walls, large permanent vacuoles and chloroplasts.

CentriolesUnder the light microscope the centriole appears as a small structure close to the nucleus (see Figure 1.3 on page 2). " e centriole is involved in nuclear division (see page 92).

Cell walls and plasmodesmataWith a light microscope, individual plant cells are more easily seen than animal cells, because they are usually larger and, unlike animal cells, surrounded by a cell wall outside the cell surface membrane. " is is relatively rigid because it contains % bres of cellulose, a polysaccharide which strengthens the wall. " e cell wall gives the cell a de% nite shape. It prevents the cell from bursting when water enters by osmosis, allowing large pressures to develop inside the cell (see page 77). Cell walls may also be reinforced with extra cellulose or with a hard material called lignin for extra strength (see xylem on page 24). Cell walls are freely permeable, allowing free movement of molecules and ions through to the cell surface membrane.

Plant cells are linked to neighbouring cells by means of % ne strands of cytoplasm called plasmodesmata (singular: plasmodesma), which pass through pore-like structures in the walls of these neighbouring cells. Movement through the pores is thought to be controlled by the structure of the pores.

VacuolesAlthough animal cells may possess small vacuoles such as phagocytic vacuoles (see page 80), which are temporary structures, mature plant cells often possess a large, permanent, central vacuole. " e plant vacuole is surrounded by a membrane, the tonoplast, which controls exchange between the vacuole and the cytoplasm. " e & uid in the vacuole is a solution of mineral salts, sugars, oxygen, carbon dioxide, pigments, enzymes and other organic compounds, including some waste products.

Vacuoles help to regulate the osmotic properties of cells (the & ow of water inwards and outwards) as well as having a wide range of other functions. For example, the pigments which colour the petals of certain & owers and parts of some vegetables, such as the red pigment of beetroots, are sometimes located in vacuoles.

66 1 Cell structure

ChloroplastsSome plant cells are able to carry out photosynthesis, because they contain chloroplasts. Chloroplasts are relatively large organelles, which are green in colour due to the presence of chlorophyll. At high magni% cations small ‘grains’, or grana (singular: granum), can be seen in the chloroplasts. During the process of photosynthesis, light is absorbed by these grana, which actually consist of stacks of membrane-bound sacs called thylakoids. Starch grains may also be visible within chloroplasts. Chloroplasts are found in the green parts of plants, mainly in the leaves.

Points to note

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

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

• Do not confuse the cell wall with the cell surface membrane. Cell walls are relatively thick and physically strong, whereas cell surface membranes are very thin. Cell walls are freely permeable, whereas cell surface membranes are partially permeable. All cells have a cell surface membrane.

• Vacuoles are not con% ned to plant cells; animal cells may have small vacuoles, such as phagocytic vacuoles (see page 80), although these are not usually permanent structures.

Fraction of a metre Unit Symbolone thousandth   0.001   1/1000   10-3 millimetre mmone millionth   0.000 001   1/1 000 000   10-6 micrometre Pmone thousand millionth   0.000 000 001   1/1 000 000 000   10-9 nanometre nm

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

We return to the di# erences between animal and plant cells as seen using the electron microscope on page 18.

Units of measurement in cell studiesIn order to measure objects in the microscopic world, we need to use very small units of measurement, which are unfamiliar to most people. According to international agreement, the International System of Units (SI units) should be used. In this system the basic unit of length is the metre (symbol, m). Additional units can be created in multiples of a thousand times larger or smaller, using standard pre% xes. For example, the pre% x kilo means 1000 times. " us 1 kilometre   1000 metres. " e units of length relevant to cell studies are shown in Table 1.1.

It is di$ cult to imagine how small these units are, but, when looking down a microscope and seeing cells clearly, we should not forget how amazingly small the cells actually are. " e smallest structure visible with the human eye is about 50–100 Pm in diameter. Your body contains about 60 million million cells, varying in size from about 5 Pm to 40 Pm. Try to imagine structures like mitochondria, which have an average diameter of 1 Pm. " e smallest cell organelles we deal with in this book, ribosomes, are only about 25 nm in diameter! You could line up about 20 000 ribosomes across the full stop at the end of this sentence.

71 Cell structure

Figure 1.8 Microscopical measurement. Three ! elds of view seen using a high-power (u40) objective lens. a An eyepiece 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.

0 10 20 30 40 50 60 70 80 90 100

stage micrometer scale(marked in 0.0 1mmand 0.1 mm divisions)

0 10 20 30 40 50 60 70 80

0 0.1 0.2

90 100

eyepiece graticulescale (arbitrary units)

cheek cells on a slideon the stage of themicroscope

eyepiece graticule inthe eyepiece of themicroscope

0 10 20 30 40 50 60 70 80 90 100

Box 1B Measuring cells

Cells and organelles can be measured with a microscope by means of an eyepiece graticule. " is is a transparent scale. It usually has 100 divisions (see Figure 1.8a). " e 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. " e cell lies between 40 and 60 on the scale. We therefore say it measures 20 eyepiece units in diameter (the di# erence 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 placed on the microscope stage and is brought into focus. " is scale may be etched onto a glass slide or printed on a transparent % lm. It commonly has subdivisions of 0.1 and 0.01 mm. " e images of the two scales can then be superimposed as shown in Figure 1.8c.

In the eyepiece graticule shown in the % gure, 100 units measure 0.25 mm. Hence, the value of each eyepiece unit is:

0 25100

0 0025.= mm

Or, converting mm to Pm:

0 25 1000100

2 5! = Pm

" e diameter of the cell shown superimposed on the scale in Figure 1.8b measures 20 eyepiece units and so its actual diameter is:

20 ! 2.5 Pm 50 Pm" is diameter is greater than that of many human cells because the cell is a & attened epithelial cell.

a

b

c

88 1 Cell structure

Electron microscopesEarlier in this chapter it was stated that by 1900, almost all the structures shown in Figures 1.3 and 1.5 (pages 2 and 3) had been discovered. " ere followed a time of frustration for microscopists, because they realised that no matter how much the design of light microscopes improved, there was a limit to how much could ever be seen using light.

In order to understand the problem, it is necessary to know something about the nature of light itself and to understand the di# erence between magnifi cation and resolution.

Magni! cationMagni" cation is the number of times larger an image is, compared with the real size of the object.

magnificff ation observed size of the imageactual size

=

or

M IA

=

where I observed size of the image (that is, what you can measure with a ruler) and A actual size (that is, the real size – for example, the size of a cell before it is magni% ed).

If you know two of these values, you can work out the third one. For example, if the observed size of the image and the magni% cation are known, you can work out the actual size: A I

M= . If you write the formula in a triangle

as shown below and cover up the value you want to % nd, it should be obvious how to do the right calculation:

I

M u A

Some worked examples are now provided.

Worked example 1 – calculating the magnifi cation of a photograph or objectTo calculate M, the magni% cation 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. " e magni% cations of the two photographs are the same. Suppose we want to know the magni% cation of the plant cell in Figure 1.9b. If we know its actual (real) length we can calculate its magni% cation using the formula M I

A= .

" e real length of the cell is 80 Pm.

Step 1Measure the length in mm of the cell in the photograph using a ruler. You should % nd that it is about 60 mm.

Step 2Convert mm to Pm. (It is easier if we % rst convert all measurements to the same units – in this case micrometres, Pm.)

1 mm  1000 Pm

so 60 mm  60 u 1000 Pm

 60 000 Pm

Step 3Use the equation to calculate the magni% cation.

magnificff ation, image size, actual size,

mm

M IA

=

=

=

6000080

µ

µ

!! 750

" e ‘u’ sign in front of the number 750 means ‘times’. We say that the magni% cation is ‘times 750’.

91 Cell structure

Figure 1.9 Photographs of the same plant cells seen a with a light microscope, b with an electron microscope, both shown at a magni! cation of about u 750.

Worked example 2 – calculating magnifi cation from a scale barFigure 1.10 shows a lymphocyte.

We can calculate the magni% cation of the lymphocyte by simply using the scale bar. All you need to do is measure the length of the scale bar and then substitute this and the length it represents into the equation.Step 1Measure the scale bar. Here, it is 36 mm.Step 2Convert mm to Pm:

36 mm 36 u 1000 Pm 36 000 Pm

Step 3Use the equation to calculate the magni% cation:

magnificff ation, image size,actual size,

mm

M IA

=

=

= !

360006

µ

µ

600066

Figure 1.10 A lymphocyte.

6 µm

a

b

1010 1 Cell structure

to distinguish between two separate points. If the two points cannot be resolved, they will be seen as one point. In practice, resolution is the amount of detail that can be seen – the greater the resolution, the greater the detail.

" e maximum resolution of a light microscope is 200 nm. " is means that if two points or objects are closer together than 200 nm they cannot be distinguished as separate.

It is possible to take a photograph such as Figure 1.9a and to magnify (enlarge) it, but we see no more detail; in other words, we do not improve resolution, even though we often enlarge photographs because they are easier to see when larger. With a microscope, magni% cation up to the limit of resolution can reveal further detail, but any further magni% cation increases blurring as well as the size of the image.

The electromagnetic spectrumHow is resolution linked with the nature of light? One of the properties of light is that it travels in waves. " e length of the waves of visible light varies, ranging from about 400 nm (violet light) to about 700 nm (red light). " e human eye can distinguish between these di# erent wavelengths, and in the brain the di# erences are converted to colour di# erences. (Colour is an invention of the brain!)

" e whole range of di# erent wavelengths is called the electromagnetic spectrum. Visible light is only one part of this spectrum. Figure 1.11 shows some of the parts of the electromagnetic spectrum. " e longer the waves, the lower their frequency (all the waves travel at the same speed, so imagine them passing a post: shorter waves pass at higher frequency). In theory, there is no limit to how short or how long the waves can be. Wavelength changes with energy: the greater the energy, the shorter the wavelength (rather like squashing a spring).

Now look at Figure 1.12, which shows a mitochondrion, some very small cell organelles called ribosomes (see page 13) and light of 400 nm wavelength, the shortest visible wavelength. " e mitochondrion is large enough to interfere with the light waves. However, the ribosomes are far too small to have any e# ect on the light waves. " e general rule is that the limit of resolution is about one half the wavelength of the radiation used to view the specimen. In other words, if an object is any smaller than half the wavelength of the radiation used to view it, it cannot be seen separately from nearby objects. " is means that the

Worked example 3 – calculating the real size of an object from its magnifi cationTo calculate A, the real or actual size of an object, we can use the following method.

Figure 1.25 on page 19 shows a plant cell magni% ed u 5600. One of the chloroplasts is labelled ‘chloroplast’ in the % gure. Suppose we want to know the actual length of this chloroplast.Step 1Measure the observed length of the image of the chloroplast (I ), in mm, using a ruler. " e maximum length is 36 mm.Step 2Convert mm to Pm:

30 mm 30 u 1000 Pm 30 000 PmStep 3Use the equation to calculate the actual length:

actual size, image size,magnificff ation,

m

A IM

=

=

=

30000600

µ

55 455 µm (to one decimal place)

SAQ 1.2

a Calculate the magni% cation of the drawing of the animal cell in Figure 1.3 on page 2.

b Calculate the actual (real) length of the bottom chloroplast in Figure 1.27 on page 19.

ResolutionLook again at Figure 1.9 (page 9). Figure 1.9a is a light micrograph (a photograph taken with a light microscope, also known as a photomicrograph). Figure 1.9b is an electron micrograph of the same cells taken at the same magni% cation (an electron micrograph is a picture taken with an electron microscope). You can see that Figure 1.9b, the electron micrograph, is much clearer. " is is because it has greater resolution. Resolution is de% ned as the ability

111 Cell structure

best resolution that can be obtained using a microscope that uses visible light (a light microscope) is 200 nm, since the shortest wavelength of visible light is 400 nm (violet light). In practice, this corresponds to a maximum useful magni% cation of about 1500 times. Ribosomes are approximately 25 nm in diameter and can therefore never be seen using light.

If an object is transparent, it will allow light waves to pass through it and therefore will still not be visible. " is is why many biological structures have to be stained before they can be seen.

The electron microscopeBiologists, faced with the problem that they would never see anything smaller than 200 nm using a light microscope, realised that the only solution would be to use radiation of a shorter wavelength than light. If you study Figure 1.11, you will see that ultraviolet light, or better still X-rays, look like possible candidates. Both ultraviolet and X-ray microscopes have been built, the latter with little success partly because of the di$ culty of focusing X-rays. A much better solution is to use electrons. Electrons are negatively charged particles which orbit the nucleus of an atom. When a metal becomes very hot, some of its electrons gain so much energy that they escape from their orbits, like a rocket escaping from Earth’s gravity. Free electrons behave like electromagnetic radiation. " ey have a very short wavelength: the greater the energy, the shorter the wavelength. Electrons are a very suitable form of radiation for microscopy for two major reasons. Firstly, their wavelength is extremely short (at least as short as that of X-rays). Secondly, because they are negatively charged, they can be focused easily using electromagnets (a magnet can be made to alter the path of the beam, the equivalent of a glass lens bending light).

Using an electron microscope, a resolution of 0.5 nm can be obtained, 400 times better than when using a light microscope.

Transmission and scanning electron microscopesTwo types of electron microscope are now in common use. " e transmission electron microscope, or TEM for

Figure 1.12 A mitochondrion and some ribosomes in the path of light waves of 400 nm length.

stained ribosomes of diameter 25 nmdo not interfere with light waves

stained mitochondrionof diameter 1000 nminterferes with light waves

wavelength400 nm

Figure 1.11 Diagram of the electromagnetic spectrum (the waves are not drawn to scale). The numbers indicate the wavelengths of the di% erent types of electromagnetic radiation. Visible light is a form of electromagnetic radiation.

400 nm 500 nm 600 nm 700 nmblueviolet yellow orange red

0.1 nm 10 nm 1000 nm

uv

105 nm 107 nm 109 nm 1011 nm 1013 nm

visible

X-rays

radio and TV waves

infrared

visible light

microwaves

gamma rays

green

E

1212 1 Cell structure

short, was the type originally developed. Here the beam of electrons is passed through the specimen before being viewed. Only those electrons that are transmitted (pass through the specimen) are seen. " is allows us to see thin sections of specimens, and thus to see inside cells. In the scanning electron microscope (SEM), on the other hand, the electron beam is used to scan the surfaces of structures, and only the refl ected beam is observed.

An example of a scanning electron micrograph is shown in Figure 1.13. " e advantage of this microscope is that surface structures can be seen. Also, great depth of % eld is obtained so that much of the specimen is in focus at the same time and a three-dimensional appearance is obtained. Such a picture would be impossible to obtain with a light microscope, even using the same magni% cation and resolution, because you would have to keep focusing up and down with the objective lens to see di# erent parts of the specimen. " e disadvantage of the SEM is that it cannot achieve the same resolution as a TEM. Resolution is between 3 nm and 20 nm.

Viewing specimens with the electron microscopeFigure 1.14 shows how an electron microscope works and Figure 1.15 shows one in use.

It is not possible to see an electron beam, so to make the image visible the electron beam has to be projected onto a & uorescent screen. " e areas hit by electrons shine brightly, giving overall a ‘black and white’ picture. " e stains used to improve the contrast of biological specimens for electron microscopy contain heavy metal atoms, which stop the passage of electrons. " e 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.

To add to the di$ culties of electron microscopy, the electron beam, and therefore the specimen and the & uorescent screen, must be in a vacuum. If electrons

Figure 1.14 How an electron microscope works.

electron gun and anode, which produce a beam of electrons

condenser electromagnetic lens, which directs the electron beam onto the specimen

specimen, which is placed on a grid

objective electromagnetic lens, which produces an image

projector electromagnetic lenses, which focus the magni!ed image onto the screen

screen or photographic plate, which shows the image of the specimen

electron beam

vacuum

pathway of electrons

Figure 1.13 False-colour SEM of the head of a cat $ ea (u 100).

E E

131 Cell structure

collided with air molecules, they would scatter, making it impossible to achieve a sharp picture. Also, water boils at room temperature in a vacuum, so all specimens must be dehydrated before being placed in the microscope. " is means that only dead material can be examined. Great e# orts are therefore made to try to preserve material in a life-like state when preparing it for the microscope.

SAQ 1.3

Explain why ribosomes are not visible using a light microscope.

Ultrastructure of an animal cell" e ‘% ne’, or detailed, structure of a cell as revealed by the electron microscope is called its ultrastructure. Figure 1.16 shows the appearance of typical animal cells as seen with an electron microscope, and Figure 1.17 on page 15 is a diagram based on many other such micrographs.

SAQ 1.4

Compare Figure 1.17 on page 15 with Figure 1.3 on page 2. Name the structures which can be seen with the electron microscope but not with the light microscope.

Structures and functions of organellesCompartmentalisation and division of labour within the cell are even more obvious with an electron microscope than with a light microscope.

We will now consider the structures and functions of some of the cell components in more detail.

Nucleus" e nucleus (Figure 1.18 on page 15) is the largest cell organelle (see also page 5). It is surrounded by two membranes known as the nuclear envelope. " e outer membrane of the nuclear envelope is continuous with the endoplasmic reticulum (Figure 1.17 on page 15). " e nuclear envelope has many small pores called nuclear pores. " ese allow and control exchange between the nucleus and the cytoplasm. Examples of substances leaving the nucleus through the pores are mRNA and ribosomes for protein synthesis. Examples of substances entering through the nuclear pores are proteins to help make ribosomes, nucleotides, ATP (aderosine triphosphate) and some hormones such as thyroid hormone T3.

Within the nucleus, the chromosomes are in a loosely coiled state known as chromatin (except during nuclear division, see Chapter 5). Chromosomes contain DNA, which is organised into functional units called genes. Genes control the activities of the cell and inheritance; thus the nucleus controls the cell’s activities. When a cell is about to divide, the nucleus divides % rst so that each new cell will have its own nucleus (Chapters 5 and 19). Also within the nucleus, the nucleolus makes ribosomes, using the information in its own DNA.

Endoplasmic reticulum and ribosomesWhen cells were % rst seen with the electron microscope, biologists were amazed to see so much detailed structure. " e existence of much of this had not been suspected. " is was particularly true of an extensive system of membranes running through the cytoplasm, which became known as the endoplasmic reticulum (ER) (Figure 1.19 on page 15 – see also Figures 1.18 on page 15 and 1.22 on page 17). " e ER is continuous with the outer membrane of the nuclear envelope (Figure 1.17).

" ere are two types of ER: rough ER and smooth ER. Rough ER is so called because it is covered with many tiny

Figure 1.15 A TEM in use.

E

1414 1 Cell structure

Golgi apparatusGolgi apparatus

lysosomelysosome

cell surfacemembranecell surfacemembrane

mitochondriamitochondria

nucleolusnucleolus

nucleusnucleus

chromatinchromatin

ribosomes

endoplasmicreticulum

endoplasmicreticulum

glycogen granulesglycogen granules

microvillusmicrovillus

ribosomes

nuclear envelopenuclear envelope

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

151 Cell structure

Figure 1.18 TEM of the nucleus of a cell from the pancreas of a bat (u 7500). The circular nucleus is surrounded by a double-layered nuclear envelope containing nuclear pores. The nucleolus is more darkly stained. Rough ER is visible in the surrounding cytoplasm.

Figure 1.19 TEM of rough ER covered with ribosomes (black dots) (u 17 000). Some free ribosomes can also be seen in the cytoplasm.

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.

microvillitwo centrioles close to thenucleus and at right anglesto each other

nucleus

Golgi vesicle

Golgi apparatus

mitochondrion

roughendoplasmicreticulum

ribosomes

lysosome

cytoplasmsmooth endoplasmicreticulum

nucleolus

cell surfacemembrane

chromatin

nuclear envelope(two membranes)

nuclear pore

1616 1 Cell structure

organelles called ribosomes. " ese are just visible as black dots in Figures 1.18 and 1.19 on page 15. At very high magni% cations they can be seen to consist of two subunits: a large and a small subunit. Ribosomes are the sites of protein synthesis (see pages 111–112). " ey can be found free in the cytoplasm as well as on the rough ER. " ey are very small, only about 25 nm in diameter. " ey are made of RNA (ribonucleic acid) and protein. " e rough ER forms an extensive system of & attened sacs spreading in sheets throughout the cell. Proteins made by the ribosomes on the rough ER enter the sacs and move through them. " e proteins are often processed in some way on their journey. Small sacs called vesicles can break o# from the ER and these can join together to form the Golgi apparatus. Proteins can be exported from the cell via the Golgi apparatus (see page 80).

Smooth ER, so called because it lacks ribosomes, has a completely di# erent function. It makes lipids and steroids, such as cholesterol and the reproductive hormones oestrogen and testosterone.

Golgi apparatus (Golgi body or Golgi complex)" e Golgi apparatus is a stack of & attened sacs (Figure 1.20). " is stack of sacs is sometimes referred to as the

Golgi body. More than one may be present in a cell. " e stack is constantly being formed at one end from vesicles which bud o# from the ER, and broken down again at the other end to form Golgi vesicles. " e stack of sacs with the associated vesicles is referred to as the Golgi apparatus or Golgi complex.

" e Golgi apparatus 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 apparatus are the addition of sugars to proteins to make molecules known as glycoproteins, and the removal of the % rst amino acid, methionine, from newly formed proteins to make a functioning protein. In plants, enzymes in the Golgi apparatus convert sugars into cell wall components. Golgi vesicles are also used to make lysosomes.

LysosomesLysosomes (Figure 1.21) are spherical sacs, surrounded by a single membrane and having no internal structure. " ey are commonly 0.1– 0.5 Pm in diameter. " ey contain digestive (hydrolytic) enzymes which must be kept separate

Figure 1.20 TEM of a Golgi apparatus. A central stack of saucer-shaped sacs can be seen budding o% small Golgi vesicles (green). These may form secretory vesicles whose contents can be released at the cell surface by exocytosis (see page 80).

Figure 1.21 Lysosomes (orange) in a mouse kidney cell (u 55 000). They contain cell structures in the process of digestion and vesicles (green). Cytoplasm is coloured blue here.

171 Cell structure

from the rest of the cell to prevent damage. Lysosomes are responsible for the breakdown (digestion) of unwanted structures such as old organelles or even whole cells, as in mammary glands after lactation (breast feeding). In white blood cells, lysosomes are used to digest bacteria (see endocytosis, page 80). Enzymes are sometimes released outside the cell – for example, in the replacement of cartilage with bone during development. " e heads of sperm contain a special lysosome, the acrosome, for digesting a path to the ovum (egg).

MitochondriaMitochondria (singular: mitochondrion) are usually about 1 Pm in diameter and can be various shapes, often sausage-shaped as in Figure 1.22. " ey are surrounded by two membranes (an envelope). " e inner of these is folded to form % nger-like cristae which project into the interior solution, or matrix.

" e main function of mitochondria is to carry out aerobic respiration. As a result of respiration, they make ATP, the universal energy carrier in cells (see Chapter 16). " ey are also involved in the synthesis of lipids (page 37).

In the 1960s it was discovered that mitochondria and chloroplasts contain ribosomes which are slightly smaller than those in the cytoplasm and are the same size as those found in bacteria. " e size of ribosomes is measured in ‘S units’, which are a measure of how fast they sediment in a centrifuge. Cytoplasmic ribosomes are 80S, while those of bacteria, mitochondria and chloroplasts are 70S. It was also discovered in the 1960s that mitochondria and chloroplasts contain small, circular DNA molecules, also like those found in bacteria. Not surprisingly, it was later proved that mitochondria and chloroplasts are, in e# ect, ancient bacteria which now live inside the larger cells typical of animals and plants (see prokaryotic and eukaryotic cells, page 18). " is is known as the endosymbiont theory. ‘Endo’ means ‘inside’ and a ‘symbiont’ is an organism which lives in a mutually bene% cial relationship with another organism. " e DNA and ribosomes of 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 dots in the mitochondrial matrix in Figure 1.22.

Cell surface membrane" e cell surface membrane is extremely thin (about 7 nm). However, at very high magni% cations, at least u 100 000, it can be seen to have three layers, described as a trilaminar appearance. " is consists of two dark lines (heavily stained) either side of a narrow, pale interior (Figure 1.23). " e membrane is partially permeable and controls exchange between the cell and its environment. Membrane structure is discussed further in Chapter 4.

MicrovilliMicrovilli (singular: microvillus) are % nger-like extensions of the cell surface membrane, typical of certain epithelial cells (cells covering surfaces of structures). " ey greatly

Figure 1.22 Mitochondrion (orange) with its double membrane (envelope); the inner membrane is folded to form cristae (u 20 000). Mitochondria are the sites of aerobic cell respiration. Note also the rough ER.

Figure 1.23 Cell surface membrane (u 250 000). At this magni! cation the membrane appears as two dark lines at the edge of the cell.

1818 1 Cell structure

increase the surface area of the cell surface membrane (see Figure 1.17 on page 15). " is is useful, for example, for absorption in the gut and for reabsorption in the proximal convoluted tubules of the kidney (see page 307).

Centrioles" e extra resolution of the electron microscope reveals that just outside the nucleus, there are really two centrioles (see Figure 1.24), not one as it appears under the light microscope (compare with Figure 1.3 on page 2). " ey lie close together at right-angles to each other. A centriole is a hollow cylinder about 0.4 Pm long, formed from a ring of short microtubules, tiny tubes made of a protein called tubulin. " ese microtubules are used as a starting point for growing the spindle microtubules for nuclear division (see page 92). Centrioles are not found in plant cells.

Ultrastructure of a plant cellAll the structures except centrioles and microvilli so far described in animal cells are also found in plant cells. " e appearance of a plant cell as seen with the electron microscope is shown in Figure 1.25 while Figure 1.26 is a diagram based on many such micrographs. " e relatively thick cell wall and the large central vacuole are obvious, as are the chloroplasts, two of which are shown in detail in Figure 1.27. " ese structures and their functions have been described on pages 5 and 6. " e electron microscope

reveals that chloroplasts contain 70S ribosomes and small, circular DNA molecules, as do mitochondria and bacteria. " is has already been discussed with mitochondria above (page 17).

SAQ 1.5

Compare Figure 1.26 with Figure 1.5 on page 3. Name the structures which can be seen with the electron microscope but not with the light microscope.

Two fundamentally di! erent types of cellAt one time it was common practice to try to classify all living organisms as either animals or plants. With advances in our knowledge of living things, it has become obvious that the living world is not that simple. Fungi and bacteria, for example, are very di# erent from animals and plants, and from each other. Eventually it was discovered that there are two fundamentally di# erent types of cell. " e most obvious di# erence between these types is that one possesses a nucleus and the other does not.

Organisms that lack nuclei are called prokaryotes (‘pro’ means before; ‘karyon’ means nucleus). All prokaryotes are now referred to as bacteria. " ey are, on average, about 1000 to 10 000 times smaller in volume than cells with nuclei, and are much simpler in structure – for example, their DNA lies free in the cytoplasm.

Organisms whose cells possess nuclei are called eukaryotes (‘eu’ means true). " eir DNA lies inside a nucleus. Eukaryotes include animals, plants, fungi and a group containing most of the unicellular eukaryotes known as protoctists. Most biologists believe that eukaryotes evolved from prokaryotes, one-and-a-half thousand million years after prokaryotes % rst appeared on Earth. We mainly study animals and plants in this book, but all eukaryotic cells have certain features in common.

A generalised prokaryotic cell is shown in Figure 1.28. A comparison of prokaryotic and eukaryotic cells is given in Table 1.2 on page 21.

Figure 1.24 Centrioles in transverse and longitudinal section (TS and LS) (u 86 000). The one on the left is seen in TS and clearly shows the nine triplets of microtubules which make up the structure.