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OXFORD IB DIplOm a pROgRam m e

2 0 1 4 ED I TI O N

BIOLO GY
C O U R S E C O M PA N I O N

Andrew Allott
David Mindorf
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3
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SCIENCE PHOTO LIBRARY; p29: Author Image; p32: Janaka Dharmasena/ research and analysis. Pettersen EF, Goddard TD, Huang CC, Couch GS,
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Continued on back page.
Contents
1 Cell Biology 7 Nucleic acids (AHL) Environmental protection 5 75
Introduction to cells 1 D NA structure and Medicine 5 82
Ultrastructure o cells 16 replication 3 43 B ioormatics 5 91
Membrane structure 25 Transcription and gene
Membrane transport 33 expression 355 C Ecology and conservation
The origin o cells 45 Translation 3 62 Species and communities 603
C ell division 51 C ommunities and
8 Metabolism, cell ecosystems 61 3
2 Molecular Biology respiration and Impacts o humans on
Molecules to metabolism 61 photosynthesis (AHL) ecosystems 62 5
Water 68 Metabolism 3 73 C onservation o biodiversity 63 5
C arbohydrates and lipids 73 C ell respiration 3 80 Population ecology 642
Proteins 87 Photosynthesis 3 89 The nitrogen and
E nzymes 96 phosphorous cycles 649
S tructure o D NA and RNA 1 05 9 Plant biology (AHL)
D NA replication, transcription Transport in the xylem D Human physiology
and translation 111 o plants 403 Human nutrition 65 9
C ell respiration 1 22 Transport in the phloem o D igestion 671
Photosynthesis 1 29 plants 41 2 Functions o the liver 678
Growth in plants 42 2 The heart 684
3 Genetics Reproduction in plants 42 9 Hormones and metabolism 694
Genes 1 41 Transport o respiratory
C hromosomes 1 49 10 Genetics and evolution gases 699
Meiosis 1 59 (AHL) Internal Assessment
Inheritance 1 68 Meiosis 43 9 (with thanks to Mark Headlee for
Genetic modication and Inheritance 445 his assistance with this chapter) 708
biotechnology 1 87 Gene pool and speciation 45 5
Index 71 3
4 Ecology 11 Animal physiology (AHL)
S pecies, communities and Antibody production and
ecosystems 2 01 vaccination 465
E nergy fow 21 3 Movement 476
C arbon cycling 220 The kidney and
C limate change 229 osmoregulation 485
S exual reproduction 499
5 Evolution and biodiversity
E vidence or evolution 2 41 A Neurobiology and
Natural selection 2 49 behaviour
C lassication and Neural development 513
biodiversity 258 The human brain 518
C ladistics 2 63 Perception o stimuli 526
Innate and learned
6 Human physiology behaviour 533
D igestion and absorption 2 79 Neuropharmacology 5 41
The blood system 2 89 Ethology 5 48
D eence against inectious
diseases 3 02 B Biotechnology and
Gas exchange 31 0 bioinformatics
Neurones and synapses 31 9 Microbiology: organisms in
Hormones, homeostasis and industry 557
reproduction 329 B iotechnology in agriculture 5 65

iii
Course book defnition The IB Learner Profle
The IB D iploma Programme course books are The aim o all IB programmes to develop
resource materials designed to support students internationally minded people who work to create
throughout their two- year D iploma Programme a better and more peaceul world. The aim o the
course o study in a particular subj ect. They will programme is to develop this person through ten
help students gain an understanding o what learner attributes, as described below.
is expected rom the study o an IB D iploma
Inquirers: They develop their natural curiosity.
Programme subj ect while presenting content in a
They acquire the skills necessary to conduct
way that illustrates the purpose and aims o the IB .
inquiry and research and snow independence in
They refect the philosophy and approach o the
learning. They actively enj oy learning and this love
IB and encourage a deep understanding o each
o learning will be sustained throughout their lives.
subj ect by making connections to wider issues and
providing opportunities or critical thinking. Knowledgeable: They explore concepts, ideas,
and issues that have local and global signicance.
The books mirror the IB philosophy o viewing the
In so doing, they acquire in-depth knowledge and
curriculum in terms o a whole- course approach;
develop understanding across a broad and balanced
the use o a wide range o resources, international
range o disciplines.
mindedness, the IB learner prole and the IB
D iploma Programme core requirements, theory Thinkers: They exercise initiative in applying
o knowledge, the extended essay, and creativity, thinking skills critically and creatively to recognize
action, service ( C AS ) . and approach complex problems, and make
reasoned, ethical decisions.
E ach book can be used in conj unction with other
materials and indeed, students o the IB are C ommunicators: They understand and express
required and encouraged to draw conclusions rom ideas and inormation condently and creatively in
a variety o resources. Suggestions or additional more than one language and in a variety o modes
and urther reading are given in each book o communication. They work eectively and
and suggestions or how to extend research are willingly in collaboration with others.
provided. Princip led: They act with integrity and honesty,
In addition, the course companions provide advice with a strong sense o airness, j ustice and respect
and guidance on the specic course assessment or the dignity o the individual, groups and
requirements and on academic honesty protocol. communities. They take responsibility or their
They are distinctive and authoritative without own action and the consequences that accompany
being prescriptive. them.
O p en-minded: They understand and appreciate
IB mission statement their own cultures and personal histories, and are
The International B accalaureate aims to develop open to the perspectives, values and traditions
inquiring, knowledgeable and caring young people o other individuals and communities. They are
who help to create a better and more peaceul accustomed to seeking and evaluating a range o
world through intercultural understanding and points o view, and are willing to grow rom the
respect. experience.
To this end the organization works with schools, C aring: They show empathy, compassion and
governments and international organizations to respect towards the needs and eelings o others.
develop challenging programmes o international They have a personal commitment to service, and
education and rigorous assessment. to act to make a positive dierence to the lives o
These programmes encourage students across the others and to the environment.
world to become active, compassionate and lielong Risk-takers: They approach unamiliar situations
learners who understand that other people, with and uncertainty with courage and orethought,
their dierences, can also be right. and have the independence o spirit to explore
new roles, ideas, and strategies. They are brave and
articulate in deending their belies.

iv
B alanced: They understand the importance o What constitutes malpractice?
intellectual, physical and emotional ballance to Malpractice is behaviour that results in, or may
achieve personal well- being or themselves and result in, you or any student gaining an unair
others. advantage in one or more assessment component.
Refective: They give thoughtul consideration Malpractice includes plagiarism and collusion.
to their own learning and experience. They are Plagiarism is defned as the representation o the
able to assess and understand their strengths and ideas or work o another person as your own. The
limitations in order to support their learning and ollowing are some o the ways to avoid plagiarism:
personal development.
 words and ideas o another person to support
ones arguments must be acknowledged
A note on academic honesty
It is o vital importance to acknowledge and  passages that are quoted verbatim must
appropriately credit the owners o inormation be enclosed within quotation marks and
when that inormation is used in your work. acknowledged
Ater all, owners o ideas ( intellectual property)  C D -Roms, email messages, web sites on the
have property rights. To have an authentic piece Internet and any other electronic media must
o work, it must be based on your individual be treated in the same way as books and
and original ideas with the work o others ully j ournals
acknowledged. Thereore, all assignments, written
or oral, completed or assessment must use your
 the sources o all photographs, maps,
own language and expression. Where sources are illustrations, computer programs, data, graphs,
used or reerred to, whether in the orm o direct audio- visual and similar material must be
quotation or paraphrase, such sources must be acknowledged i they are not your own work
appropriately acknowledged.  works o art, whether music, flm dance,
How do I acknowledge the work of others? theatre arts or visual arts and where the
The way that you acknowledge that you have used creative use o a part o a work takes place, the
the ideas o other people is through the use o original artist must be acknowledged.
ootnotes and bibliographies. C ollusion is defned as supporting malpractice by
Footnotes ( placed at the bottom o a page) or another student. This includes:
endnotes ( placed at the end o a document) are  allowing your work to be copied or submitted
to be provided when you quote or paraphrase or assessment by another student
rom another document, or closely summarize the
 duplicating work or dierent assessment
inormation provided in another document. You
components and/or diploma requirements.
do not need to provide a ootnote or inormation
that is part o a body o knowledge. That is, O ther orms o malp ractice include any action
defnitions do not need to be ootnoted as they are that gives you an unair advantage or aects the
part o the assumed knowledge. results o another student. Examples include,
taking unauthorized material into an examination
B ibliograp hies should include a ormal list o the
room, misconduct during an examination and
resources that you used in your work. Formal
alsiying a C AS record.
means that you should use one o the several
accepted orms o presentation. This usually
involves separating the resources that you use
into dierent categories ( e.g. books, magazines,
newspaper articles, internet-based resources, C ds
and works o art) and providing ull inormation
as to how a reader or viewer o your work can
fnd the same inormation. A bibliography is
compulsory in the E xtended Essay.

v
Using your IB Biology
Online Resources
What is Kerboodle?
Kerboodle is an online learning platorm. I your school has a
subscription to IB B iology Kerboodle O nline Resources you will be able
to access a huge bank o resources, assessments, and presentations to
guide you through this course.

What is in your Kerboodle Online Resources?


There are three main areas or students on the IB B iology Kerboodle:
planning, resources, and assessment.

Resources
There a hundreds o extra resources available on the IB B iology
Kerboodle O nline. You can use these at home or in the classroom to
develop your skills and knowledge as you progress through the course.
Watch videos and animations o experiments, difcult concepts, and
science in action.
Hundreds o worksheets  read articles, perorm experiments and
simulations, practice your skills, or use your knowledge to answer
questions.
Look at galleries o images rom the book and see their details close up.
Find out more by looking at recommended sites on the Internet,
answer questions, or do more research.

Planning
B e prepared or the practical work and your internal assessment with
extra resources on the IB B iology Kerboodle online.
Learn about the dierent skills that you need to perorm an investigation.
Plan and prepare experiments o your own.
Learn how to analyse data and draw conclusions successully
and accurately.

One of hundreds of worksheets. Practical skills presentation.


vi
Assessment
C lick on the assessment tab to check your knowledge or revise or your
examinations. Here you will fnd lots o interactive quizzes and exam-
style practice questions.
Formative tests: use these to check your comprehension, theres one
auto-marked quiz or every sub-topic. E valuate how confdent you
eel about a sub-topic, then complete the test. You will have two
attempts at each question and get eedback ater every question. The
marks are automatically reported in the markbook, so you can see
how you progress throughout the year.
Summative tests: use these to practice or your exams or as revision,
theres one auto- marked quiz or every topic. Work through the test
as i it were an examination  go back and change any questions you
arent sure about until you are happy, then submit the test or a fnal
mark. The marks are automatically reported in the markbook, so you
can see where you may need more practice.
Assessment practice: use these to practice answering the longer
written questions you will come across when you are examined.
These worksheets can be printed out and perormed as a timed test.

Don't forget!
You can also fnd extra resources on our ree website
www.oxfordsecondary.co.uk/ib-biology
Here you can fnd all o the answers
and even more practice questions.

vii
Introduction Nature of science
This book is a companion or students o B iology
Here you can explore the methods o science and
in the International B accalaureate D iploma
some o the knowledge issues that are associated
Programme.
with scientifc endeavour. This is done using
B iology is the most popular choice o science careully selected examples, including biological
subj ect as part o the IB diploma. The study o research that led to paradigm shits in our
biology should lead students to appreciate the understanding o the natural world.
interconnectedness o lie within the biosphere.
With a ocus on understanding the nature o
science, IB B iology will allow you to develop a
Theory of Knowledge
level o scientifc literacy that will better prepare These short sections have headings that are equivocal
you to act on issues o local and global concern, ` knowledge questions. The text that follows often
with a ull understanding o the scientifc point details one possible answer to the knowledge question.
o view. We encourage you draw on these examples of
The structure o this book is closely based on the knowledge issues in your TOK essays. Of course, much
biology programme in the S ubj ect Guide. S ub- of the material elsewhere in the book, particularly in the
headings restate the specifc assessment statements. nature of science sections, can be used to prompt TOK
Topics 1  6 explain in detail the C ore material
discussions.
that is common to both S L and HL courses. Topics
7  1 1 explain the AHL ( additional higher level
material) . Topics A, B , C and D cover the content
activity
o the options. All topics include the ollowing
A variety of short topics are included under this heading
elements:
with the focus in all cases on active learning. We
encourage you research these topics yourself, using
Understanding information available in textbooks or on the Internet. The
The specifcs o the content requirements or aim is to promote an independent approach to learning.
each sub- topic are covered in detail. C oncepts are We believe that the optimal approach to learning is to
presented in ways that will promote enduring be active  the more that you do for yourself, guided by
understanding. your teacher, the better you will learn.

Applications Data-based questions


These sections help you to develop your
These questions involve studying and analysing data
understanding by studying a specifc illustrative
from biological research  this type of question appears
example or learning about a signifcant experiment
in both Paper 2 and Paper 3 for SL and HL IB Biology.
in the history o biology.
Answers to these questions can be found at
www.oxfordsecondary.co.uk/ib-biology
Skills topics
These sections encourage you to apply your
understanding through practical activities End -of-Topic Questions
and analysis o results rom classic biological At the end o each topic you will fnd a range o
research. In some cases this involves instructions questions, including both past IB B iology exam
or handling data rom experiments and also questions and new questions. Answers can be
use o IC T. Some o the skills sections involve ound at www.oxordsecondary. co.uk/ib- biology
experiments with known outcomes, aimed at
promoting understanding through doing and
seeing. O thers involve ideas or experimental
work with unknown outcomes, where you can
defne the problem and the methods. These are a
valuable opportunities to build the skills that are
assessed in IA ( see page 708) .

viii
1 CE LL B I O LO GY
Introduction
There is an unbroken chain o lie rom the rst in prokaryotes and eukaryotes. While evolution
cells on Earth to all cells ound in organisms has resulted in a biological world o enormous
alive today. Eukaryotes have a much more diversity, the study o cells shows us that
complex cell structure than prokaryotes. The there are also universal eatures. For example,
evolution o multicellular organisms allowed the fuid and dynamic structure o biological
cell specialization and cell replacement. C ell membranes allows them to control the
division is essential but is carried out dierently composition o cells.

1.1 Introduction to cells


Understanding Applications
 According to the cell theory, living organisms
 Questioning the cell theory using atypical
are composed o cells. examples, including striated muscle, giant
 Organisms consisting o only one cell carry out algae and aseptate ungal hyphae.
all unctions o lie in that cell.  Investigation o unctions o lie in
 Surace area to volume ratio is important in the Paramecium and one named photosynthetic
limitation o cell size. unicellular organism.
 Multicellular organisms have properties  Use o stem cells to treat Stargardts disease
that emerge rom the interaction o their and one other named condition.
cellular components.  Ethics o the therapeutic use o stem cells rom
 Specialized tissues can develop by cell specially created embryos, rom the umbilical
dierentiation in multicellular organisms. cord blood o a new-born baby and rom an
 Dierentiation involves the expression o some adults own tissues.
genes and not others in a cells genome.
 The capacity o stem cells to divide and
dierentiate along dierent pathways is
necessary in embryonic development. It also
makes stem cells suitable or therapeutic uses.

Nature of science Skills


 Looking or trends and discrepancies: although  Use o a light microscope to investigate the
most organisms conorm to cell theory, there structure o cells and tissues.
are exceptions.  Drawing cell structures as seen with the
 Ethical implications o research: research light microscope.
involving stem cells is growing in importance  Calculation o the magnifcation o drawings
and raises ethical issues. and the actual size o structures shown in
drawings or micrographs.

1
1 C E LL B I O LO G Y

The cell theory


Living organisms are composed of cells.
The internal structure of living organisms is very intricate and is built
up from very small individual parts. O rgans such as the kidney and
the eye are easily visible. If they are dissected we can see that large
organs are made of a number of different tissues, but until microscopes
were invented little or nothing was discovered about the structure of
tissues. From the 1 7th century onwards biologists examined tissues
from both plants and animals using microscopes. Although there was
much variation, certain features were seen again and again. A theory
was developed to explain the basic features of structure  the cell theory.
This states that cells are the fundamental building blocks of all living
organisms. The smallest organisms are unicellular  they consist of j ust
one cell. Larger organisms are multicellular  they are composed of
many cells.
C ells vary considerably in size and shape but they share certain common
features:
 Every living cell is surrounded by a membrane, which separates the
cell contents from everything else outside.
 C ells contain genetic material which stores all of the instructions
needed for the cells activities.
 Many of these activities are chemical reactions, catalysed by enzymes
produced inside the cell.
 C ells have their own energy release system that powers all of the
cells activities.
S o, cells can be thought of as the smallest living structures  nothing
smaller can survive.

 Figure 1 Coloured scanning electron micrograph (SEM) of a human embryo on the tip of a pin
2
1 .1 I n tro d u ctI o n to ce lls

Exceptions to the cell theory


Looking for trends and discrepancies: although most
organisms conform to cell theory, there are exceptions.
An early stage in scientifc investigation is to look or trends  things
that appear to be ound generally rather than j ust in specifc cases.
These trends can lead to the development o a theory. A scientifc
theory is a way o interpreting the natural world. Theories allow us to
make predictions. S ometimes exceptions to a general trend are ound.
These are called discrepancies. S cientists have to j udge whether the
discrepancies are common or serious enough to make predictions too
unreliable to be useul. The theory is then discarded.
The cell theory is an example o where scientists have looked or trends  Figure 2 Robert Hookes drawing of cork cells
and discrepancies. Robert Hooke was the frst to use the word cell or
structures in living organisms. He did this in 1 665 ater examining cork
and other parts o plants. Ater describing cells in cork he wrote this: Aiviy
Nor is this kind of texture peculiar to cork only, for upon
examination with my microscope I have found that the pith of the
Elder or almost any other tree, the inner pith of the Cany hollow
stems of several other vegetables: as of Fennel, Carrets, Daucus,
Bur-docks, Teasels, Fearn, some kind of Reeds etc. have much
such a kind of Schematisme, as I have lately shown that of cork.
S o Hooke wasnt content with looking at j ust one type o plant
tissue  he looked at many and discovered a general trend. S ince
Hookes day biologists have looked at tissues rom a huge variety o
living organisms. Many o these tissues have been ound to consist
 Figure 3 What is the unit of life:
o cells, so the cell theory has not been discarded. However, some
the boy or his cells?
discrepancies have been discovered  organisms or parts o organisms
that do not consist o typical cells. More discrepancies may be These two answers represent
discovered, but it is extremely unlikely that the cell theory will ever the holistic and the reductionist
be discarded, because so many tissues do consist o cells. approach in biology.

image viewed here


Using light microscopes
eyepiece lens
Use of a light microscope to investigate the
structure of cells and tissues.
coarse-focusing
Try to improve your skill at using microscopes as knob
much as you can. ne-focusing
turret knob
 Learn the names o parts o the microscope. objective lens
 Understand how to ocus the microscope to get the specimen
best possible image. stage
 Look ater your microscope so it stays in perect light from mirror
working order. or light bulb
 Know how to troubleshoot problems.

 Figure 4 Compound light microscope

3
1 C E LL B I O LO G Y

Focusing Types of slide


 Put the slide on the stage, with the most The slides that we examine with a microscope can
promising region exactly in the middle o the be permanent or temporary.
hole in the stage that the light comes through.
Making permanent slides is very skilled and takes
 Always ocus at low power rst even i a long time, so these slides are normally made
eventually you need high power magnication. by experts. Permanent slides o tissues are made
 Focus with the larger coarse- ocusing knobs using very thin slices o tissue.
rst, then when you have nearly got the Making temporary slides is quicker and easier so
image in ocus make it really sharp using the we can do this or ourselves.
smaller ne- ocusing knobs.
Examining and drawing plant and
 I you want to increase the magnication, animal cells
move the slide so the most promising region is
Almost all cells are too small to be seen with
exactly in the middle o the eld o view and
the naked eye, so a microscope is needed to
then change to a higher magnication lens.
study them.
Looking after your microscope
It is usually easy to see whether a cell is rom a
 Always ocus by moving the lens and the
plant or an animal, even though there are many
specimen urther apart, never closer to each other.
dierent cell types in both the plant and animal
 Make sure that the slide is clean and dry kingdoms.
beore putting it on the stage.  Place the cells on the slide in a layer not more
 Never touch the suraces o the lenses with than one cell thick.
your ngers or anything else.  Add a drop o water or stain.
 C arry the microscope careully with a  C areully lower a cover slip onto the drop. Try
hand under it to support its weight securely.
to avoid trapping any air bubbles.
Troubleshooting  Remove excess fuid or stain by putting the
Problem: Nothing is visible when I try to ocus. slide inside a olded piece o paper towel and
pressing lightly on the cover slip.
Solution: Make sure the specimen is actually
under the lens, by careully positioning the slide. It is best to examine the slide rst using low
It is easier to nd the specimen i you ocus at low power. Move the slide to get the most promising
power rst. areas in the middle o the eld o view and then
move up to high power. D raw a ew cells, so you
Problem: A circle with a thick black rim is visible. remember their structure.
Solution: There is an air bubble on the slide. cover carefully lower the
Ignore it and try to improve your technique or slip cover slip
making slides so that there are no air bubbles.
Problem: There are blurred parts o the image cells stain or water
even when I ocus it as well as I can.
gently squeeze
Solution: Either the lenses or the slide have dirt to remove exces
on them. Ask your teacher to clean it. uid
Problem: The image is very dark.
cover slip
Solution: Increase the amount o light passing
through the specimen by adj usting the diaphragm. slide
folded
Problem: The image looks rather bleached. a er towel

Solution: D ecrease the amount o light passing  Figure 5 Making a temporary mount
through the specimen by adj usting the diaphragm.

4
1 .1 I n tro d u ctI o n to ce lls

1 Moss leaf 2 B anana fruit cell 3 Mammalian liver cell


10 m 5 m
20 m

Use a moss plant with very Scrape a small amount o the S crape cells rom a reshly cut
thin leaves. Mount a single sot tissue rom a banana and surace o liver ( not previously
lea in a drop o water or place on a slide. Mount in a rozen) . S mear onto a slide and
methylene blue stain. drop o iodine solution. add methylene blue to stain.
4 Leaf lower epidermis 5 Human cheek cell 6 White blood cell

20 m

10 m 2 m

Peel the lower epidermis o a S crape cells rom the inside o A thin layer o mammalian
lea. The cell drawn here was your cheek with a cotton bud. blood can be smeared over a
rom Valeriana. Mount in water S mear them on a slide and add slide and stained with
or in methylene blue. methylene blue to stain. Leishmans stain.
 Figure 6 Plant and animal cell drawings

Drawing cells
Drawing cell structures as seen with the light microscope.
C areul drawings are a useul way o recording the structure o cells or other biological structures.
Usually the lines on the drawing represent the edges o structures. D o not show unnecessary
detail and only use aint shading. D rawings o structures seen using a microscope will be larger
than the structures actually are  the drawing shows them magnifed. O n page 6 the method or
calculating the magnifcation o a drawing is explained. E verything on a drawing should be shown to
the same magnifcation.
a) Use a sharp pencil with b) Join up lines careully c) D raw lines reehand,
a hard lead to draw to orm continuous but use a ruler or
single sharp lines. structures such as cells labelling lines.
cell cell

bad good bad good bad good


 Figure 7 Examples of drawing styles

5
1 C E LL B I O LO G Y

Calculation o magnifcation and actual size


Calculation o the magnifcation o drawings and the actual size o structures shown
in drawings or micrographs.
When we look down a microscope the structures It is very important when using this ormula
that we see appear larger than they actually to make sure that the units or the size o the
are. The microscope is magniying them. Most image and actual size o the specimen are the
microscopes allow us to magniy specimens by same. They could both be millimetres ( mm) or
two or three dierent actors. This is done by micrometres ( m) but they must not be dierent
rotating the turret to switch rom one obj ective or the calculation will be wrong. Millimetres can
lens to another. A typical school microscope has be converted to micrometres by multiplying by
three levels o magnifcation: one thousand. Micrometres can be converted to
millimetres by dividing by one thousand.
  40 ( low power)
S cale bars are sometimes put on micrographs
  1 00 ( medium power)
or drawings, or j ust alongside them. These are
  400 ( high power) straight lines, with the actual size that the scale
I we take a photo down a microscope, we can bar represents. For example, i there was a
magniy the image even more. A photo taken down 1 0 mm long scale bar on a micrograph with a
a microscope is called a micrograph. There are magnifcation o  1 0, 000 the scale bar would
many micrographs in this book, including electron have a label o 1 m.
micrographs taken using an electron microscope. EXAMPLE:
When we draw a specimen, we can make the The length o an image is 3 0 mm. It represents
drawing larger or smaller, so the magnifcation a structure that has an actual size o 3 m.
o the drawing isnt necessarily the same as the D etermine the magnifcation o the image.
magnifcation o the microscope. Either:
To fnd the magnifcation o a micrograph or a 3 0 mm = 3 0  1 0 - 3 m
drawing we need to know two things: the size o 3 m = 3  1 0 - 6 m
the image ( in the drawing or the micrograph) and 30  1 0 - 3
the actual size o the specimen. This ormula is Magnifcation = _
3  1 0-6
used or the calculation: = 1 0, 000 
size o image
magnifcation = ___ Or:
actual size o specimen 3 0 mm = 3 0, 000 m
I we know the size o the image and the 3 0, 000
magnifcation, we can calculate the actual size Magnifcation = _
3
o a specimen. = 1 0, 000 

Data-based questions
1 a) D etermine the magnifcation o the string
o Thiomargarita cells in fgure 8, i the
scale bar represents 0.2 mm [3 ]
b) Determine the width o the string
o cells. [2]

 Figure 8 Thiomargarita

6
1 .1 I n tro d u ctI o n to ce lls

2 In fgure 9 the actual length o the b) D etermine the length o the


mitochondrion is 8 m. cheek cell. [2 ]
a) D etermine the magnifcation o this
electron micrograph. [2 ]
b) C alculate how long a 5 m scale bar
would be on this electron micrograph. [2 ]
c) Determine the width o the
mitochondrion. [1 ]  Figure 10 Human cheek cell
4 a) Using the width o the hens egg as a
guide, estimate the actual length o the
ostrich egg ( fgure 1 1 ) . [2 ]
b) E stimate the magnifcation o
the image. [2 ]

 Figure 9 Mitochondrion
3 The magnifcation o the human cheek cell
rom a compound microscope ( fgure 1 0)
is 2 , 000  .
a) C alculate how long a 2 0 m scale bar
would be on the image. [2 ]
 Figure 11 Ostrich egg

Testing the cell theory


Questioning the cell theory using atypical examples, including striated muscle,
giant algae and aseptate fungal hyphae.
To test the cell theory you should look at In humans they have an average length o
the structure o as many living organisms as about 3 0 mm, whereas other human cells are
you can, using a microscope. Instructions or mostly less than 0.03 mm in length. Instead
microscope use are given on page 4. In each o having one nucleus they have many,
case you should ask the question, D oes the sometimes as many as several hundred.
organism or tissue ft the trend stated in the cell
theory by consisting o one or more cells?
Three atypical examples are worth considering:
 Striated muscle is the type o tissue that
we use to change the position o our body.
The building blocks o this tissue are muscle
fbres, which are similar in some ways to
cells. They are surrounded by a membrane
and are ormed by division o pre-existing
cells. They have their own genetic material
and their own energy release system.
However muscle fbres are ar rom typical.
They are much larger than most animal cells.  Figure 12 Striated muscle fbres

7
1 C E LL B I O LO G Y

 Fungi consist o narrow thread-like structures


called hyphae. These hyphae are usually
white in colour and have a fuy appearance.
They have a cell membrane and, outside it, a
cell wall. In some types o ungi the hyphae
are divided up into small cell-like sections by
cross walls called septa. However, in aseptate
ungi there are no septa. Each hypha is an
uninterrupted tube-like structure with many
 Figure 13 Aseptate hypha
nuclei spread along it.
 Algae are organisms that eed themselves by
photosynthesis and store their genes inside
nuclei, but they are simpler in their structure
and organization than plants. Many algae consist
o one microscopic cell. There are vast numbers
o these unicellular algae in the oceans and they
orm the basis o most marine ood chains. Less
common are some algae that grow to a much
larger size, yet they still seem to be single cells.
They are known as giant algae. Acetabularia is
one example. It can grow to a length o as much
as 1 00 mm, despite only having one nucleus.
I a new organism with a length o 1 00 mm
was discovered, we would certainly expect it to
consist o many cells, not just one.  Figure 14 Giant alga

Unicellular organisms
Organisms consisting of only one cell carry out all
functions of life in that cell.
The unctions o lie are things that all organisms must do to stay alive.
S ome organisms consist o only one cell. This cell thereore has to carry
out all the unctions o lie. B ecause o this the structure o unicellular
organisms is more complex than most cells in multicellular organisms.
Unicellular organisms carry out at least seven unctions o lie:
 Nutrition  obtaining ood, to provide energy and the materials
needed or growth.
 Metabolism  chemical reactions inside the cell, including cell
respiration to release energy.
 Growth  an irreversible increase in size.
 Response  the ability to react to changes in the environment.
 Excretion  getting rid o the waste products o metabolism.
 Homeostasis  keeping conditions inside the organism within
tolerable limits.
 Reproduction  producing ospring either sexually or asexually.
Many unicellular organisms also have a method o movement, but some
remain in a xed position or merely drit in water or air currents.
8
1 .1 I n tro d u ctI o n to ce lls

Limitations on cell size


Surface area to volume ratio is important in the limitation
of cell size.
In the cytoplasm of cells, large numbers of chemical reactions take place.
These reactions are known collectively as the metabolism of the cell. The
rate of these reactions ( the metabolic rate of the cell) is proportional to
the volume of the cell.
For metabolism to continue, substances used in the reactions must be
absorbed by the cell and waste products must be removed. S ubstances
move into and out of cells through the plasma membrane at the surface
of the cell. The rate at which substances cross this membrane depends on
its surface area.
The surface area to volume ratio of a cell is therefore very important. If
same cube
the ratio is too small then substances will not enter the cell as quickly as unfolded
they are required and waste products will accumulate because they are
produced more rapidly than they can be excreted.
Surface area to volume ratio is also important in relation to heat
 Figure 15 Volume and surace area
production and loss. If the ratio is too small then cells may overheat
o a cube
because the metabolism produces heat faster than it is lost over the
cells surface.

Functions of life in unicellular organisms


Investigation of functions of life in Paramecium and one named photosynthetic
unicellular organism.
Paramecium is a unicellular organism that can be cultured quite easily in the laboratory. Alternatively collect
some pond water and use a centrifuge to concentrate the organisms in it to see if Paramecium is present.
Place a drop of culture solution containing Paramecium on a microscope slide.
Add a cover slip and examine the slide with a microscope.

The nucleus o the cell can divide to produce The contractile vacuoles at each end o the cell ll up with water and
the extra nuclei that are needed when the cell then expel it through the plasma membrane o the cell, to keep the
reproduces. Oten the reproduction is asexual with cells water content within tolerable limits.
the parent cell dividing to orm two daughter cells.
Food vacuoles contain smaller Metabolic reactions take place
organisms that the Paramecium in the cytoplasm, including the
has consumed. These are gradually reactions that release energy
digested and the nutrients are by respiration. Enzymes in the
absorbed into the cytoplasm where cytoplasm are the catalysts that
they provide energy and materials cause these reactions to happen.
needed or growth.

The cell membrane controls Beating o the cilia moves the


what chemicals enter and leave. Paramecium through the water
It allows the entry o oxygen or and this can be controlled by the
respiration. Excretion happens cell so that it moves in a particular
simply by waste products direction in response to changes
difusing out through the in the environment.
membrane.

 Figure 16 Paramecium

9
1 C E LL B I O LO G Y

Chlamydomonas is a unicellular alga that lives in soil and freshwater habitats. It has been used widely for
research into cell and molecular biology. Although it is green in colour and carries out photosynthesis it is
not a true plant and its cell wall is not made of cellulose.

The nucleus o the cell


can divide to produce The contractile vacuoles
genetically identical at the base o the fagella
nuclei or asexual ll up with water and then
reproduction. Nuclei can expel it through the plasma
also use and divide membrane o the cell, to keep
to carry out a sexual the cells water content within
orm o reproduction. tolerable limits.
In this image, the
nucleus is concealed by
chloroplasts. Photosynthesis occurs inside
chloroplasts in the cytoplasm.
Metabolic reactions take Carbon dioxide can be converted
place in the cytoplasm, into the compounds needed
with enzymes present to or growth here, but in the dark
speed them up. carbon compounds rom other
organisms are sometimes
absorbed through the cell
membrane i they are available.
The cell wall is reely
permeable and it is the
membrane inside it that Beating o the two fagella
controls what chemicals moves the Chlamydomonas
enter and leave. Oxygen through the water. A light-
is a waste product o sensitive eyespot allows
photosynthesis and is the cell to sense where the
excreted by diusing out brightest light is and respond
through the membrane. by swimming towards it.

 Figure 17 Chlamydomonas

Multicellular organisms
Multicellular organisms have properties that emerge from
the interaction of their cellular components.
S ome unicellular organisms live together in colonies, for example a
type of alga called Volvox aureus. E ach colony consists of a ball made of
a protein gel, with 5 00 or more identical cells attached to its surface.
Figure 1 8 shows two colonies, with daughter colonies forming inside
them. Although the cells are cooperating, they are not fused to form a
single cell mass and so are not a single organism.
O rganisms consisting of a single mass of cells, fused together, are
 Figure 18 Volvox colonies multicellular. O ne of the most intensively researched multicellular
organisms is a worm called Caenorhabditis elegans. The adult body is about
one millimetre long and it is made up of exactly 95 9 cells. This might
seem like a large number, but most multicellular organisms have far
more cells. There are about ten million million cells in an adult human
body and even more in organisms such as oak trees or whales.
Although very well known to biologists, Caenorhabditis elegans has no
common name and lives unseen in decomposing organic matter. It
feeds on the bacteria that cause decomposition. C. elegans has a mouth,
pharynx, intestine and anus. It is hermaphrodite so has both male and
female reproductive organs. Almost a third of the cells are neurons, or

10
1 .1 I n tro d u ctI o n to ce lls

nerve cells. Most o these neurons are located at the ront end o the
worm in a structure that can be regarded as the animals brain.
toK
Although the brain in C. elegans coordinates responses to the worms Hw a w i wh  m i
environment, it does not control how individual cells develop. The cells b ha ah?
in this and other multicellular organisms can be regarded as cooperative An emergent property o a system is
groups, without any cells in the group acting as a leader or supervisor. not a property o any one component
It is remarkable how individual cells in a group can organize themselves o the system, but it is a property o
and interact with each other to orm a living organism with distinctive the system as a whole. Emergence
overall properties. The characteristics o the whole organism, including reers to how complex systems and
the act that it is alive, are known as emergent properties. patterns arise rom many small and
E mergent properties arise rom the interaction o the component parts relatively simple interactions. We
o a complex structure. We sometimes sum this up with the phrase: cannot thereore necessarily predict
the whole is greater than the sum o its parts. A simple example emergent properties by studying
o an emergent property was described in a C hinese philosophical each part o a system separately (an
text written more than 2 , 5 00 years ago: Pots are fashioned from approach known as reductionism) .
clay. But its the hollow that makes the pot work.  S o, in biology we Molecular biology is an example o the
can carry out research by studying component parts, but we must success that a reductionist approach
remember that some bigger things result rom interactions between can have. Many processes occurring in
these components. living organisms have been explained
at a molecular level. However, many
argue that reductionism is less useul
Cell diferentiation in multicellular organisms in the study o emergent properties
Specialized tissues can develop by cell dierentiation in including intelligence, consciousness
and other aspects o psychology. The
multicellular organisms. interconnectivity o the components
In multicellular organisms dierent cells perorm dierent unctions. This in cases like these is at least as
is sometimes called division o labour. In simple terms, a unction is a job important as the unctioning o each
or a role. For example the unction o a red blood cell is to carry oxygen, individual component.
and the unction o a rod cell in the retina o the eye is to absorb light and One approach that has been used to
then transmit impulses to the brain. Oten a group o cells specialize in the study interconnectivity and emergent
same way to perorm the same unction. They are called a tissue. properties is computer modelling. In
B y becoming specialized, the cells in a tissue can carry out their role both animal behaviour and ecology,
more efciently than i they had many dierent roles. They can develop a programme known as the Game o
the ideal structure, with the enzymes needed to carry out all o the Lie has been used. It was devised
chemical reactions associated with the unction. The development by John Conway and is available on
o cells in dierent ways to carry out specifc unctions is called the Internet. Test the Game o Lie by
dierentiation. In humans, 2 2 0 distinctively dierent highly specialized creating initial confgurations o cells and
cell types have been recognized, all o which develop by dierentiation. seeing how they evolve. Research ways
in which the model has been applied.

Gene expression and cell diferentiation


Dierentiation involves the expression o some genes and
not others in a cells genome.
There are many dierent cell types in a multicellular organism but they
all have the same set o genes. The 2 2 0 cell types in the human body
have the same set o genes, despite large dierences in their structure
and activities. To take an example, rod cells in the retina o the eye
produce a pigment that absorbs light. Without it, the rod cell would not
be able to do its j ob o sensing light. A lens cell in the eye produces no
pigments and is transparent. I it did contain pigments, less light would

11
1 C E LL B I O LO G Y

pass through the lens and our vision would be worse. While they are
developing, both cell types contain the genes for making the pigment,
but these genes are only used in the rod cell.
This is the usual situation  cells do not j ust have genes with the
instructions that they need, they have genes needed to specialize in
every possible way. There are approximately 2 5 , 000 genes in the human
genome, and these genes are all present in a body cell. However, in most
cell types less than half of the genes will ever be needed or used.
When a gene is being used in a cell, we say that the gene is being
expressed. In simple terms, the gene is switched on and the information
in it is used to make a protein or other gene product. The development
of a cell involves switching on particular genes and expressing them, but
not others. C ell differentiation happens because a different sequence of
genes is expressed in different cell types. The control of gene expression
is therefore the key to development.
An extreme example of differentiation involves a large family of genes in
humans that carry the information for making receptors for odorants 
smells. These genes are only expressed in cells in the skin inside the
nose, called olfactory receptor cells. Each of these cells expresses j ust
one of the genes and so makes one type of receptor to detect one type
of odorant. This is how we can distinguish between so many different
smells. Richard Axel and Linda B uck were given the Nobel Prize in 2 004
for their work on this system.

Stem cells
The capacity o stem cells to divide and diferentiate
along diferent pathways is necessary in embryonic
development. It also makes stem cells suitable or
therapeutic uses.
A new animal life starts when a sperm fertilizes an egg cell to produce a
zygote. An embryo is formed when the zygote divides to give two cells.
This two- cell embryo divides again to produce a four- cell embryo, then
eight, sixteen and so on. At these early stages in embryonic development
the cells are capable of dividing many times to produce large amounts
of tissue. They are also extremely versatile and can differentiate along
different pathways into any of the cell types found in that particular
animal. In the 1 9th century, the name stem cell was given to the zygote
and the cells of the early embryo, meaning that all the tissues of the
adult stem from them.
S tem cells have two key properties that have made them one of the most
active areas of research in biology and medicine today.
 S tem cells can divide again and again to produce copious quantities
of new cells. They are therefore useful for the growth of tissues or
the replacement of cells that have been lost or damaged.
 S tem cells are not fully differentiated. They can differentiate in
 Figure 19 Embryonic stem cells different ways, to produce different cell types.

12
1 .1 I n tro d u ctI o n to ce lls

Embryonic stem cells are thereore potentially very useul. They could
be used to produce regenerated tissue, such as skin or people who
have suered burns. They could provide a means o healing diseases
such as type 1 diabetes where a particular cell type has been lost or is
malunctioning. They might even be used in the uture to grow whole
replacement organs  hearts or kidneys, or example. These types o use
are called therapeutic, because they provide therapies or diseases or
other health problems.
There are also non-therapeutic uses or embryonic stem cells. One possibility
is to use them to produce large quantities o striated muscle fbres, or meat,
or human consumption. The bee burgers o the uture may thereore be
produced rom stem cells, without the need to rear and slaughter cattle.
It is the early stage embryonic stem cells that are the most versatile.
Gradually during embryo development the cells commit themselves to a
pattern o dierentiation. This involves a series o points at which a cell
decides whether to develop along one pathway or another. Eventually
each cell becomes committed to develop into one specifc cell type. Once
committed, a cell may still be able to divide, but all o these cells will
dierentiate in the same way and they are no longer stem cells.
Small numbers o cells remain as stem cells, however, and they are still
present in the adult body. They are present in many human tissues,
including bone marrow, skin and liver. They give some human tissues
considerable powers o regeneration and repair. The stem cells in other
tissues only allow limited repair  brain, kidney and heart or example.

Therapeutic uses of stem cells


Use of stem cells to treat Stargardts disease and one other named condition.
There are a ew current uses o stem cells to treat Researchers have developed methods or making
diseases, and a huge range o possible uture uses, embryonic stem cells develop into retina cells.
many o which are being actively researched. Two This was done initially with mouse cells, which
examples are given here: one involving embryonic were then injected into the eyes o mice that had
stem cells and one using adult stem cells. a condition similar to Stargardts disease. The
injected cells were not rejected, did not develop
Stargardts disease
into tumours or cause any other problems. The
The ull name o this disease is S targardts macular cells moved to the retina where they attached
dystrophy. It is a genetic disease that develops themselves and remained. Very encouragingly, they
in children between the ages o six and twelve. caused an improvement in the vision o the mice.
Most cases are due to a recessive mutation o
a gene called AB C A4. This causes a membrane In November 2 01 0, researchers in the United
protein used or active transport in retina cells to S tates got approval or trials in humans. A woman
malunction. As a consequence, photoreceptive in her 5 0s with S targardts disease was treated by
cells in the retina degenerate. These are the cells having 5 0, 000 retina cells derived rom embryonic
that detect light, so vision becomes progressively stem cells inj ected into her eyes. Again the cells
worse. The loss o vision can be severe enough or attached to the retina and remained there during
the person to be registered as blind. the our- month trial. There was an improvement
in her vision, and no harmul side eects.

13
1 C E LL B I O LO G Y

Further trials with larger numbers o patients can be done by treating the patient with
are needed, but ater these initial trials at least, chemicals that kill dividing cells. The procedure
we can be optimistic about the development o is known as chemotherapy. However, to remain
treatments or S targardts disease using embryonic healthy in the long term the patient must be
stem cells. able to produce the white blood cells needed
to ght disease. S tem cells that can produce
blood cells must be present, but they are killed
by chemotherapy. The ollowing procedure is
thereore used:
 A large needle is inserted into a large bone,
usually the pelvis, and fuid is removed rom
the bone marrow.
 S tem cells are extracted rom this fuid and are
stored by reezing them. They are adult stem
cells and only have the potential or producing
blood cells.
 Figure 20 Stargardts disease
 A high dose o chemotherapy drugs is given
leukemia to the patient, to kill all the cancer cells in
This disease is a type o cancer. All cancers start the bone marrow. The bone marrow loses its
when mutations occur in genes that control cell ability to produce blood cells.
division. For a cancer to develop, several specic
 The stem cells are then returned to the
mutations must occur in these genes in one cell.
patients body. They re- establish themselves
This is very unlikely to happen, but as there are
in the bone marrow, multiply and start to
huge numbers o cells in the body, the overall
produce red and white blood cells.
chance becomes much larger. More than a quarter
o a million cases o leukemia are diagnosed each In many cases this procedure cures the leukemia
year globally and there are over 2 00, 000 deaths completely.
rom the disease.
Once the cancer-inducing mutations have
occurred in a cell, it grows and divides repeatedly,
producing more and more cells. Leukemia involves
the production o abnormally large numbers o
white blood cells. In most cancers, the cancer cells
orm a lump or tumour but this does not happen
with leukemia. White blood cells are produced in
the bone marrow, a sot tissue in the hollow centre
o large bones such as the emur. They are then
released into the blood, both in normal conditions
and when excessive numbers are produced with
leukemia. A normal adult white blood cell count is
between 4, 000 and 1 1 ,000 per mm 3 o blood. In a
person with leukemia this number rises higher and
higher. C ounts above 30,000 per mm 3 suggest that
a person may have leukemia. I there are more
than 1 00, 000 per mm 3 it is likely that the person
has acute leukemia.
To cure leukemia, the cancer cells in the bone
marrow that are producing excessive numbers
o white blood cells must be destroyed. This  Figure 21 Removal of stem cells from bone marrow

14
1 .1 I n tro d u ctI o n to ce lls

The ethics of stem cell research


Ethical implications o research: research involving stem cells is growing in
importance and raises ethical issues.
S tem cell research has been very controversial. D ecisions about whether research is ethically
Many ethical obj ections have been raised. acceptable must be based on a clear understanding
S cientists should always consider the ethical o the science involved. S ome people dismiss all
implications o their research beore doing it. stem cell research as unethical, but this shows a
S ome o the research that was carried out in the misunderstanding o the dierent possible sources
past would not be considered ethically acceptable o the stem cells being used. In the next section,
today, such as medical research carried out on three possible sources o stem cells and the ethics
patients without their inormed consent. o research involving them are discussed.

Sources of stem cells and the ethics of using them


Ethics o the therapeutic use o stem cells rom specially created embryos, rom
the umbilical cord blood o a new-born baby and rom an adults own tissues.
Stem cells can be obtained rom a variety o sources.
 E mbryos can be deliberately created by and stored or possible use later in the
ertilizing egg cells with sperm and allowing babys lie.
the resulting zygote to develop or a ew days  S tem cells can be obtained rom some adult
until it has between our and sixteen cells. All tissues such as bone marrow.
o the cells are embryonic stem cells.
These types o stem cell vary in their properties and
 B lood can be extracted rom the umbilical thereore in their potential or therapeutic use. The
cord o a new- born baby and stem cells table below gives some properties o the three types,
obtained rom it. The cells can be rozen to give the scientifc basis or an ethical assessment.

embyi m  c b m  A m 
 Almost unlimited growth potential.  Easily obtained and stored.  Difcult to obtain as there are
 Can dierentiate into any type in  Commercial collection and very ew o them and they are
the body. storage services already buried deep in tissues.
 More risk o becoming tumour available.  Less growth potential than
cells than with adult stem cells,  Fully compatible with the tissues o embryonic stem cells.
including teratomas that contain the adult that grows rom the baby,  Less chance o malignant
dierent tissue types. so no rejection problems occur. tumours developing than rom
 Less chance o genetic damage  Limited capacity to dierentiate embryonic stem cells.
due to the accumulation o into dierent cell types  only  Limited capacity to dierentiate
mutations than with adult naturally develop into blood into dierent cell types.
stem cells. cells, but research may lead to  Fully compatible with the adults
 Likely to be genetically dierent production o other types. tissues, so rejection problems do
rom an adult patient receiving  Limited quantities o stem cells not occur.
the tissue.
rom one babys cord.  Removal o stem cells does not
 Removal o cells rom the
 The umbilical cord is discarded kill the adult rom which the cells
embryo kills it, unless only one
whether or not stem cells are are taken.
or two cells are taken.
taken rom it.

15
1 C E LL B I O LO G Y

Stem cell research has been very controversial. have lived has been denied its chance of living.
Many ethical obj ections have been raised. There However, a counterargument is that it is unethical
are most obj ections to the use of embryonic stem to create human lives solely for the purpose of
cells, because current techniques usually involve obtaining stem cells. Also, IVF involves hormone
the death of the embryo when the stem cells are treatment of women, with some associated risk, as
taken. The main question is whether an early well as an invasive surgical procedure for removal
stage embryo is as much a human individual as a of eggs from the ovary. If women are paid for
new- born baby, in which case killing the embryo supplying eggs for IVF this could lead to the
is undoubtedly unethical. exploitation of vulnerable groups such as college
students.
When does a human life begin? There are different
views on this. Some consider that when the We mu st no t fo rge t
sperm fertilizes the egg, a human life has begun. e thical argume nts
Others say that early stage embryos have not yet in favo ur o f the
developed human characteristics and cannot suffer u se o f e mb ryo nic
pain, so they should be thought of simply as groups ste m ce lls. The y
of stem cells. Some suggest that a human life truly have the p o te ntial
begins when there is a heartbeat, or bone tissue or to allo w me tho ds
brain activity. These stages take place after a few o f tre atme nt
weeks of development. Another view is that it is fo r dise ase s and
only when the embryo has developed into a fetus disab ilitie s that are
that is capable of surviving outside the uterus. cu rre ntly incu rab le ,
so the y co u ld gre atly
Some scientists argue that if embryos are specially
re du ce the su ffe ring  Figure 22 Harvesting umbilical
created by in vitro fertilization (IVF) in order to
o f so me individuals. cord blood
obtain stem cells, no human that would otherwise

1.2 ultrastrctre of cells


Understanding Applications
 Prokaryotes have a simple cell structure
 The structure and unction o organelles within
without compartments. exocrine gland cells o the pancreas.
 Eukaryotes have a compartmentalized cell
 The structure and unction o organelles within
structure. palisade mesophyll cells o the lea.
 Prokaryotes divide by binary fssion.
 Electron microscopes have a much higher
resolution than light microscopes.

Nature of science Skills


 Developments in scientifc research ollow  Drawing the ultrastructure o prokaryotic cells
improvements in apparatus: the invention based on electron micrographs.
o electron microscopes led to greater  Drawing the ultrastructure o eukaryotic cells
understanding o cell structure. based on electron micrographs.
 Interpretation o electron micrographs to
identiy organelles and deduce the unction o
specialized cells.
16
1 . 2 u lt r A s t r u c t u r e o f c e l l s

th invnin  h n mip


Developments in scientifc research ollow improvements in apparatus: the
invention o electron microscopes led to greater understanding o cell structure.
Much o the progress in biology over the last 1 50 images to be produced o things as small as
years has ollowed improvements in the design o 0.001 m  2 00 times smaller than with light
microscopes. In the second hal o the 1 9th century microscopes. The structure o eukaryotic cells was
improved light microscopes allowed the discovery ound to be ar more intricate than most biologists
o bacteria and other unicellular organisms. had expected and many previous ideas were shown
C hromosomes were seen or the rst time and the to be wrong. For example, in the 1 890s the light
processes o mitosis, meiosis and gamete ormation microscope had revealed darker green areas in the
were discovered. The basis o sexual reproduction, chloroplast. They were called grana and interpreted
which had previously eluded William Harvey and as droplets o chlorophyll. The electron microscope
many other biologists, was seen to be the usion o showed that grana are in act stacks o fattened
gametes and subsequent development o embryos. membrane sacs, with the chlorophyll located in
The complexity o organs such as the kidney was the membranes. Whereas mitochondria appear as
revealed and mitochondria, chloroplasts and other tiny structureless rods or spheres under the light
structures were discovered within cells. microscope, the electron microscope revealed them
to have an intricate internal membrane structure.
There was a limit to the discoveries that could
be made though. For technical reasons that are The electron microscopes revealed what is
explained later in this sub-topic, light microscopes now called the ultrastructure o cells, including
cannot produce clear images o structures smaller previously unknown eatures. Ribosomes,
than 0.2 micrometres (m) . (A micrometre is lysosomes and the endoplasmic reticulum were all
a thousandth o a millimetre.) Many biological discovered and named in the 1 95 0s, or example.
structures are smaller than this. For example, It is unlikely that there are structures as signicant
membranes in cells are about 0.01 m thick. as these still to be discovered, but improvements
Progress was hampered until a dierent type o in the design o electron microscopes continue
microscope was invented  the electron microscope. and each improvement allows new discoveries to
be made. A recent example, described in sub-
Electron microscopes were developed in Germany
topic 8.2 , is electron tomography  a method o
during the 1 930s and came into use in research
producing 3 - D images by electron microscopy.
laboratories in the 1 940s and 5 0s. They allowed

The resolution of electron microscopes


Electron microscopes have a much higher resolution
than light microscopes.
I we look at a tree with unaided eyes we can see its individual leaves, but
we cannot see the cells within its leaves. The unaided eye can see things
with a size o 0.1 mm as separate objects, but no smaller. To see the cells
within the lea we need to use a light microscope. This allows us to see
things with a size o down to about 0.2 m as separate objects, so cells can
become individually visible  they can be distinguished.
Making the separate parts o an obj ect distinguishable by eye is called
resolution.
The maximum resolution o a light microscope is 0. 2 m, which is 2 00
nanometres ( nm) . However powerul the lenses o a light microscope
are, the resolution cannot be higher than this because it is limited by the
wavelength o light ( 400700 nm) . I we try to resolve smaller obj ects by  Figure 1 An electron microscope
in use
17
1 C E LL B I O LO G Y

making lenses with greater magnifcation, we fnd that it is impossible to


ocus them properly and get a blurred image. This is why the maximum
magnifcation with light microscopes is usually  400.
Beams o electrons have a much shorter wavelength, so electron microscopes
have a much higher resolution. The resolution o modern electron
microscopes is 0.001 m or 1 nm. Electron microscopes thereore have a
resolution that is 200 times greater than light microscopes. This is why light
microscopes reveal the structure o cells, but electron microscopes reveal the
ultrastructure. It explains why light microscopes were needed to see bacteria
with a size o 1 micrometre, but viruses with a diameter o 0.1 micrometres
could not be seen until electron microscopes had been invented.

resolutio
Millimetes Miometes naometes
(mm) (m) (m)
Unaided eyes 0.1 100 100,000
Light microscopes 0.0002 0.2 200
Electron microscopes 0.000001 0.001 1
Ativity
commee ad siee
While still a young student in
Prokaryotic cell structure
Berlin in the late 1920s Ernst Prokaryotes have a simple cell structure without
Ruska developed magnetic compartments .
coils that could ocus beams
All organisms can be divided into two groups according to their cell
o electrons. He worked on the
structure. Eukaryotes have a compartment within the cell that contains
idea o using these lenses to
the chromosomes. It is called the nucleus and is bounded by a nuclear
obtain an image as in a light
envelope consisting o a double layer o membrane. Prokaryotes do not
microscope, but with electron
have a nucleus.
beams instead o light. During
the 1930s he developed and Prokaryotes were the frst organisms to evolve on Earth and they still
refned this technology. By have the simplest cell structure. They are mostly small in size and
1939 Ruska had designed are ound almost everywhere  in soil, in water, on our skin, in our
the frst commercial electron intestines and even in pools o hot water in volcanic areas.
microscope. In 1986 he was All cells have a cell membrane, but some cells, including prokaryotes,
awarded the Nobel Prize in also have a cell wall outside the cell membrane. This is a much
Physics or this pioneering thicker and stronger structure than the membrane. It protects the cell,
work. Ruska worked with the maintains its shape and prevents it rom bursting. In prokaryotes the cell
German frm Siemens. Other wall contains peptidoglycan. It is oten reerred to as being extracellular.
companies in Britain, Canada
and the United States also As no nucleus is present in a prokaryotic cell its interior is entirely flled
developed and manuactured with cytoplasm. The cytoplasm is not divided into compartments by
electron microscopes. membranes  it is one uninterrupted chamber. The structure is thereore
simpler than in eukaryotic cells, though we must remember that it is still
 Scientists in dierent
very complex in terms o the biochemicals that are present, including
countries usually
many enzymes.
cooperate with each
other but commercial O rganelles are present in the cytoplasm o eukaryotic cells that are
companies do not. What analogous to the organs o multi- cellular organisms in that they are
are the reasons or this distinct structures with specialized unctions. Prokaryotes do not have
dierence? cytoplasmic organelles apart rom ribosomes. Their size, measured in
S vedberg units ( S ) is 70S, which is smaller than those o eukaryotes.

18
1 . 2 u lt r A s t r u c t u r e o f c e l l s

Part o the cytoplasm appears lighter than the rest in many electron
micrographs. This region contains the DNA o the cell, usually in the orm o
one circular DNA molecule. The DNA is not associated with proteins, which
explains the lighter appearance compared with other parts o the cytoplasm
that contain enzymes and ribosomes. This lighter area o the cell is called the
nucleoid  meaning nucleus-like as it contains DNA but is not a true nucleus.

Cell division in prokaryotes


Prokaryotes divide by binary fssion.
All living organisms need to produce new cells. They can only do this by
division o pre- existing cells. C ell division in prokaryotic cells is called
binary fssion and it is used or asexual reproduction. The single circular
chromosome is replicated and the two copies o the chromosome move
to opposite ends o the cell. D ivision o the cytoplasm o the cell quickly
ollows. E ach o the daughter cells contains one copy o the chromosome
so they are genetically identical.

dawing pkayi 


Draw the ultrastructure o prokaryotic cells based on
electron micrographs. Aiviy
B ecause prokaryotes are mostly very small, their internal structure oh nam 
cannot be seen using a light microscope. It is only with much higher pkay
magnifcation in electron micrographs that we can see the details o
Biologists sometimes use
the structure, called the ultrastructure. D rawings o the ultrastructure
the term bacteria instead
o prokaryotes are thereore based on electron micrographs.
o prokaryote. This may
Shown below and on the next page are two electron micrographs o not always be appropriate
E. coli, a bacterium ound in our intestines. One o them is a thin section because the term
and shows the internal structure. The other has been prepared by a prokaryote encompasses
dierent technique and shows the external structure. A drawing o each a larger group o organisms
is also shown. B y comparing the drawings with the electron micrographs than true bacteria
you can learn how to identiy structures within prokaryotic cells. (Eubacteria) . It also includes
E lectron micrograp h of Escherichia coli (1 2 m in length)
organisms in another group
called the Archaea.
There is a group o
photosynthetic organisms
that used to be called
blue-green algae, but their
cell structure is prokaryotic
and algae are eukaryotic.
This problem has been
D rawing to help interp ret the electron micrograp h
solved by renaming them as
nucleoid (region Cyanobacteria.
ribosomes cell wall plasma membrane cytoplasm containing naked DNA)
 What problems are
caused by scientists
using dierent words
or things than non-
scientists?

19
1 C E LL B I O LO G Y

Electron micrograph of Escherichia coli showing surface features

pili

agellum

Shown below is another micrograph o a prokaryote. You can use it to


practice your skill at drawing the ultrastructure o prokaryotic cells. You
can also fnd other electron micrographs o prokaryotic cells on the internet
and try drawing these. There is no need to spend a long time drawing
many copies o a particular structure, such as the ribosomes. You can
indicate their appearance in one small representative part o the cytoplasm
and annotate your drawing to say that they are ound elsewhere.

Activity
Garlic cells and
compartmentalization
Garlic cells store a harmless
sulphur-containing
compound called alliin in
their vacuoles. They store
an enzyme called alliinase
in other parts o the cell.
Alliinase converts alliin into
a compound called allicin,
which has a very strong
smell and favour and is
toxic to some herbivores.  Figure 2 Brucella abortus (Bangs bacillus) , 2 m in length
This reaction occurs when
herbivores bite into garlic
and damage cells, mixing the
enzyme and its substrate.
Eukaryotic cell structure
Perhaps surprisingly, many Eukaryotes have a compartmentalized cell structure.
humans like the favour, but to Eukaryotic cells have a much more complicated internal structure than
get it garlic must be crushed prokaryotic cells. Whereas the cytoplasm o a prokaryotic cell is one
or cut, not used whole. undivided space, eukaryotic cells are compartmentalized. This means
 You can test this by that they are divided up by partitions into compartments. The partitions
smelling a whole garlic are single or double membranes.
bulb, then cutting or
The most important o these compartments is the nucleus. It contains
crushing it and smelling
the cells chromosomes. The compartments in the cytoplasm are known
it again.
as organelles. Just as each organ in an animals body is specialized

20
1 . 2 u lt r A s t r u c t u r e o f c e l l s

to perform a particular role, each organelle in a eukaryotic cell has a


distinctive structure and function.
There are several advantages in being compartmentalized:
 Enzymes and substrates for a particular process can be much more
concentrated than if they were spread throughout the cytoplasm.
 S ubstances that could cause damage to the cell can be kept inside the
membrane of an organelle. For example, the digestive enzymes of
a lysosome could digest and kill a cell, if they were not safely stored
inside the lysosome membrane.
 C onditions such as pH can be maintained at an ideal level for a
particular process, which may be different to the levels needed for
other processes in a cell.
 O rganelles with their contents can be moved around within the cell.

dawig kayi 


Draw the ultrastructure o eukaryotic cells based on electron micrographs.
The ultrastructure of eukaryotic cells is very The table below contains an electron micrograph
complex and it is often best to draw only part of each of the commonly occurring organelles,
of a cell. Your drawing is an interpretation of with a drawing of the structure. B rief notes on
the structure, so you need to understand the recognition features and the function of each
structure of the organelles that might be present. organelle are included.

n The nuclear membrane is double and has pores


double nuclear through it. The nucleus contains the chromosomes,
membrane nuclear pores consisting o DNA associated with histone proteins.
Uncoiled chromosomes are spread through the
nucleus and are called chromatin. There are oten
densely staining areas o chromatin around the edge
o the nucleus. The nucleus is where DNA is replicated
and transcribed to orm mRNA, which is exported via
dense chromatin
chromatin the nuclear pores to the cytoplasm.

rgh pami The rER consists o fattened membrane sacs, called


im cisternae. Attached to the outside o these cisternae
ribosomes are ribosomes. They are larger than in prokaryotes and
are classied as 80S. The main unction o the rER is to
synthesize protein or secretion rom the cell. Protein
synthesized by the ribosomes o the rER passes into
its cisternae and is then carried by vesicles, which bud
o and are moved to the Golgi apparatus.
cisterna

21
1 C E LL B I O LO G Y

Gogi apparatus This organelle consists o fattened membrane sacs


cisterna called cisternae, like rER. However the cisternae are
not as long, are oten curved, do not have attached
ribosomes and have many vesicles nearby. The Golgi
apparatus processes proteins brought in vesicles
vesicles rom the rER. Most o these proteins are then carried in
vesicles to the plasma membrane or secretion.

lysosome These are approximately spherical with a single


digestive enzymes membrane. They are ormed rom Golgi vesicles. They
contain high concentrations o protein, which makes
them densely staining in electron micrographs. They
contain digestive enzymes, which can be used to
break down ingested ood in vesicles or break down
organelles in the cell or even the whole cell.
lysosome membrane

Mitohondrion A double membrane surrounds mitochondria, with


inner outer the inner o these membranes invaginated to orm
membrane membrane structures called cristae. The fuid inside is called the
matrix. The shape o mitochondria is variable but is
usually spherical or ovoid. They produce ATP or the
cell by aerobic cell respiration. Fat is digested here i it
is being used as an energy source in the cell.
crista matrix

free ribosomes These appear as dark granules in the cytoplasm and


are not surrounded by a membrane. They have the
same size as ribosomes attached to the rER  about
20nm in diameter, and known as 80S. Free ribosomes
synthesize protein, releasing it to work in the
cytoplasm, as enzymes or in other ways. Ribosomes
are constructed in a region o the nucleus called
the nucleolus.
choropast A double membrane surrounds the chloroplast. Inside
starch grain are stacks o thylakoids, which are fattened sacs o
membrane. The shape o chloroplasts is variable but
stroma is usually spherical or ovoid. They produce glucose
and a wide variety o other organic compounds by
double photosynthesis. Starch grains may be present inside
membrane chloroplasts i they have been photosynthesizing
thylakoid rapidly.
Vauoes and These are organelles that consist simply o a single
vesies membrane with fuid inside. Many plant cells have
vacuole large vacuoles that occupy more than hal o the cell
containing food volume. Some animals absorb oods rom outside
and digest them inside vacuoles. Some unicellular
organisms use vacuoles to expel excess water.
large vacuole Vesicles are very small vacuoles used to transport
vesicles materials inside the cell.

22
1 . 2 u lt r A s t r u c t u r e o  c e l l s

Mib and In the cytoplasm o cells there are small cylindrical


ni bres called microtubules that have a variety o roles,
including moving chromosomes during cell division.
triple Animal cells have structures called centrioles, which
microtubules consist o two groups o nine triple microtubules.
Centrioles orm an anchor point or microtubules
during cell division and also or microtubules inside
cilia and fagella.
ciia and faga These are whip-like structures projecting rom the
cell surace. They contain a ring o nine double
microtubules plus two central ones. Flagella are larger
and usually only one is present, as in a sperm. Cilia are
smaller and many are present. Cilia and fagella can be
double used or locomotion. Cilia can be also be used to create
plasma microtubule a current in the fuid next to the cell.
membrane

The electron micrograph below shows a liver cell  Using your understanding of these organelles,
with labels to identify some of the organelles that draw the whole cell to show its ultrastructure.
are present.
free
mitochondrion nucleus ribosomes

FPO
<839211_ph1.2.15>

rough endoplasmic Golgi lysosome


reticulum a aratus
 Figure 3 Electron micrograph of part of a liver cell

23
1 C E LL B I O LO G Y

Exocrine gland cells of the pancreas


The structure and function of organelles within exocrine gland cells of
the pancreas.
Gland cells secrete substances  they release them
through their plasma membrane. There are two
types of gland cells in the pancreas. E ndocrine
cells secrete hormones into the bloodstream.
E xocrine gland cells in the pancreas secrete
digestive enzymes into a duct that carries them to
the small intestine where they digest foods. FPO
Enzymes are proteins, so the exocrine gland cells <Insert 839211_
have organelles needed to synthesize proteins ph1.2.16>
in large quantities, process them to make them
ready for secretion, transport them to the plasma
membrane and then release them. The electron
micrograph on the right shows these organelles:
plasma membrane Golgi apparatus
mitochondrion vesicles
nucleus lysosomes
rough ER  Figure 4 Electron micrograph of pancreas cell

Palisade mesophyll cells


The structure and function of organelles
within palisade mesophyll cells of the leaf.
The function of the leaf is photosynthesis 
producing organic compounds from carbon
dioxide and other simple inorganic compounds,
using light energy. The cell type that carries
out most photosynthesis in the leaf is palisade
mesophyll. The shape of these cells is roughly
cylindrical. Like all living plant cells the cell
is surrounded by a cell wall, with a plasma
membrane inside it. The electron micrograph
on the right shows the organelles that a palisade
mesophyll cell contains:
cell wall
plasma membrane
chloroplasts
mitochondrion
vacuole
 Figure 5 Electron micrograph of palisade mesophyll cell
nucleus

24
1 . 3 M e M b rAn e s tru ctu r e

Ipig h  of kayoi ll


Interpret electron micrographs to identiy organelles and deduce the unction
o specialized cells.
I the organelles in a eukaryotic cell can be
identifed and their unction is known, it is oten
possible to deduce the overall unction o the cell.
 S tudy the electron micrographs in fgures 6, 7
and 8. Identiy the organelles that are present
and try to deduce the unction o each cell.

 Figure 7

 Figure 6
 Figure 8

1.3 Mma 


Understanding Applications
 Phospholipids orm bilayers in water due to the
 Cholesterol in mammalian membranes reduces
amphipathic properties o phospholipid molecules. membrane fuidity and permeability to some
 Membrane proteins are diverse in terms o solutes.
structure, position in the membrane and unction.
 Cholesterol is a component o animal cell
membranes.

Nature of science Skills


 Using models as representations o the  Drawing the fuid mosaic model.
real world: there are alternative models o  Analysis o evidence rom electron microscopy that
membrane structure. led to the proposal o the DavsonDanielli model.
 Falsication o theories with one theory being  Analysis o the alsication o the DavsonDanielli
superseded by another: evidence alsied the model that led to the SingerNicolson model
DavsonDanielli model.

25
1 C E LL B I O LO G Y

OH
hydrophilic
Phospholipid bilayers
O P O
phosphate
O head
Phospholipids form bilayers in water due to the
H C H H H amphipathic properties of phospholipid molecules.
C C
Some substances are attracted to water  they are hydrop hilic.
O O H
C O C O O ther substances are not attracted to water  they are hydrop hobic.
H C H H C H
Phospholipids are unusual because part o a phospholipid molecule is
H C H H C H
hydrophilic and part is hydrophobic. Substances with this property are
H C H H C H described as amp hip athic.
H C H H C H
H C H H C H The hydrophilic part o a phospholipid is the phosphate group. The
H C H H C H hydrophobic part consists o two hydrocarbon chains. The chemical
H C H H C H
structure o phospholipids is shown in fgure 1 .
hydrophobic
C H H C H hydrocarbon The structure can be represented simply using a circle or the phosphate
tails group and two lines or the hydrocarbon chains.
C H H C H
H C H H C H
H C H C H
H C H C H
H C H H C H
 Figure 2 Simplifed diagram o a phospholipid molecule
H C H H C H
H C H H C H
The two parts o the molecule are oten called phosphate heads and
H C H H C H
hydrocarbon tails. When phospholipids are mixed with water the
H C H H C H phosphate heads are attracted to the water but the hydrocarbon
H H tails are attracted to each other, but not to water. B ecause o this the
 Figure 1 The molecular structure phospholipids become arranged into double layers, with the hydrophobic
o a phospholipid. The phosphate hydrocarbon tails acing inwards towards each other and the hydrophilic
oten has other hydrophilic groups heads acing the water on either side. These double layers are called
attached to it, but these are not phospholipid bilayers. They are stable structures and they orm the basis
shown in this diagram o all cell membranes.

hydrophilic phosphate head

hydrophobic hydrocarbon tails


phospholipid
bilayer

 Figure 3 Simplifed diagram o a phospholipid bilayer

Models of membrane structure


Using models as representations of the real world: there are alternative models of
membrane structure.
In the 1 9 2 0 s, Gorter and Grendel extracted arranged in a monolayer was twice as large as
phospholipids rom the plasma membrane the area o plasma membrane. They deduced
o red blood cells and calculated that the that the membrane contained a bilayer o
area that the phospholipids occupied when phospholipids. There were several errors in

26
1 . 3 M e M b rAn e s tru ctu r e

their methods but luckily these cancelled each band between. Proteins appear dark in electron
other out and there is now very strong evidence micrographs and phospholipids appear light,
or cell membranes being based on phospholipid so this appearance tted the D avson- D anielli
bilayers. model.
Membranes also contain protein and Gorter Another model o membrane structure was
and Grendels model did not explain where proposed in 1 966 by Singer and Nicolson. In this
this is located. In the 1 9 3 0s D avson and model the proteins occupy a variety o positions
D anielli proposed layers o protein adj acent in the membrane. Peripheral proteins are attached
to the phospholipid bilayer, on both sides o to the inner or outer surace. Integral proteins are
the membrane. They proposed this sandwich embedded in the phospholipid bilayer, in some
model because they thought it would explain cases with parts protruding out rom the bilayer
how membranes, despite being very thin, are on one or both sides. The proteins are likened to
a very eective barrier to the movement o the tiles in a mosaic. B ecause the phospholipid
some substances. High magnication electron molecules are ree to move in each o the two
micrographs o membranes were made in layers o the bilayer, the proteins are also able to
the 1 9 5 0s, which showed a railroad track move. This gives the model its name  the fuid
appearance  two dark lines with a lighter mosaic model.

Polm wih h davodailli mol


Falsifcation o theories with one theory being superseded by another: evidence
alsifed the DavsonDanielli model.
The D avsonD anielli model o membrane
structure was accepted by most cell biologists
or about 3 0 years. Results o many experiments
tted the model including X- ray diraction studies
and electron microscopy.
In the 1 95 0s and 60s some experimental evidence
accumulated that did not t with the D avson
D anielli model:
 Freeze-etched electron micrograp hs.
This technique involves rapid reezing o
cells and then racturing them. The racture
occurs along lines o weakness, including the
centre o membranes. Globular structures
scattered through reeze- etched images o
the centre o membranes were interpreted as
transmembrane proteins.
 S tructure of membrane p roteins.
Improvements in biochemical techniques
allowed proteins to be extracted rom  Figure 4 Freeze-etched electron micrograph of nuclear
membranes. They were ound to be very membranes, with nuclear pores visible and vesicles in the
varied in size and globular in shape so surrounding cytoplasm. The diagram on page 28 shows the line
of fracture through the centre of the inner and outer nuclear
were unlike the type o structural protein
membranes. Transmembrane proteins are visible in both of the
that would orm continuous layers on the
membranes

27
1 C E LL B I O LO G Y

periphery o the membrane. Also the proteins replacement was needed that tted the evidence
were hydrophobic on at least part o their and the model that became widely accepted was
surace so they would be attracted to the the S ingerNicolson fuid mosaic model. It has
hydrocarbon tails o the phospholipids in the been the leading model or over ty years but
centre o the membrane. it would be unwise to assume that it will never
be superseded. There are already some suggested
 Fluorescent antibody tagging. Red or
modications o the model.
green fuorescent markers were attached to
antibodies that bind to membrane proteins. An important maxim or scientists is Think it
The membrane proteins o some cells were possible that you might be mistaken. Advances
tagged with red markers and other cells in science happen because scientists rej ect
with green markers. The cells were used dogma and instead search continually or better
together. Within 40 minutes the red and understanding.
green markers were mixed throughout the
cytoplasm
membrane o the used cell. This showed that
membrane proteins are ree to move within
the membrane rather than being xed in a
peripheral layer.
Taken together, this experimental evidence nucleus inner membrane
alsied the D avsonD anielli model. A outer membrane

Evidence for and against the DavsonDanielli model of


membrane structure
Analysis of evidence from electron microscopy that led to the proposal of the
DavsonDanielli model.
Figure 5 shows the plasma membrane o a red
blood cell and some o the cytoplasm near the
edge o the cell.
1 . D escribe the appearance o the plasma
membrane. [2 ]
2 . Explain how this appearance suggested that the
membrane had a central region o phospholipid
with layers o protein on either side. [2 ]
3 . Suggest reasons or the dark grainy appearance
o the cytoplasm o the red blood cell. [2 ]
4. C alculate the magnication o the electron
micrograph assuming that the thickness o
the membrane is 1 0 nanometres. [3 ]
The two sets o data- based questions that ollow
are based on the types o data that were
used to alsiy the D avsonD anielli model o
membrane structure.  Figure 5 TEM of plasma membrane of a red blood cell

28
1 . 3 M e M b rAn e s tru ctu r e

daa-a qio: Membranes in Difusion o proteins in membranes


reeze-etched electron micrographs Frye and Edidin used an elegant technique
Figure 6 shows a reeze- etched electron to obtain evidence or the fuid nature o
micrograph image o part o a cell. It was membranes. They attached fuorescent markers
prepared by Proessor Horst Robenek o to membrane proteins  green markers to mouse
Mnster University. cells and red markers to human cells. In both
cases, spherical cells growing in tissue culture
were used. The marked mouse and human cells
were then used together. At rst, the used cells
had one green hemisphere and one red one,
but over the minutes ollowing usion, the red
and green markers gradually merged, until they
were completely mixed throughout the whole o
the cell membrane. B locking o ATP production
did not prevent this mixing ( ATP supplies energy
or active processes in the cell) .

tim af cll wih mak flly mix/%


fio /
rl rl rl rl Ma
mi
1 2 3 4
5 0 0  
10 3 0  
25 40 54  

 Figure 6
40 87 88 93 100
120 100   
1 In all o the ractured membranes in the
micrograph small granules are visible. 1 C alculate the mean percentage o cells with
a) S tate what these granules are. [2 ] markers ully mixed or each time ater
usion. [4]
b) E xplain the signicance o these
granules in the investigation o 2 Plot a graph o the results, including range
membrane structure. [3 ] bars or times where there was variation
in the results. To do this you plot the highest
2 O ne o the membranes that surround and lowest results with a small bar and
the nucleus is visible on the let o the j oin these bars with a ruled line. You
micrograph. D educe whether it is the should also plot the mean result with a
inner or outer nuclear membrane. ( Always cross. This will lie on the range bar. [4]
give your reasons when asked to deduce
something.) [2 ] 3 D escribe the trend shown by the graph. [1 ]

3 Identiy three mitochondria visible in 4 Explain whether the results t the


the micrograph, either using labels or by D avsonD anielli model or the
describing their positions. [2 ] S ingerNicolson model more closely. [2 ]

4 Explain the evidence rom the micrograph 5 Explain the benet o plotting range bars
that this cell was processing proteins in on graphs. [2 ]
its cytoplasm. [2 ] 6 During this experiment the cells were
Extension questions on this topic can be ound incubated at 37 C . Suggest a reason or the
at www.oxordsecondary. co.uk/ib- biology researchers choosing this temperature. [1 ]

29
1 C E LL B I O LO G Y

7 The experiment was repeated at dierent


temperatures. Figure 7 shows the results. 100

% of cells with markers


fully mixed after 40 minutes
1
1
Explain the trends shown in the graph or 1
1
temperatures between 1 5 and 3 5 C . [2 ] 1
1

8 Explain the trends shown in the graph or 50 1


temperatures below 1 5 C . [2 ] 1

9 When ATP synthesis was blocked in the cells,


the mixing o the red and green markers still 1 1
1
1
occurred. E xplain what conclusion can be 0 5 15 25 35
drawn rom this. [1 ] incubation temperature (C)

1 0 Predict, with reasons, the results o the  Figure 7 Eect o temperature on the
experiment i it was repeated using cells rate o diusion o fuorescent markers
rom arctic fsh rather than rom mice in membranes
or humans. [1 ]

Membrane proteins
Membrane proteins are diverse in terms o structure,
position in the membrane and unction.
C ell membranes have a wide range o unctions. The primary unction
is to orm a barrier through which ions and hydrophilic molecules
cannot easily pass. This is carried out by the phospholipid bilayer. Almost
all other unctions are carried out by proteins in the membrane. Six
examples are listed in table 1 .

functions o membrane proteins


Hormone binding sites (also called hormone receptors) , or example the insulin
receptor. Figure 8 shows an example.
Immobilized enzymes with the active site on the outside, or example in the small
intestine.
Cell adhesion to orm tight junctions between groups o cells in tissues and organs.
Cell-to-cell communication, or example receptors or neurotransmitters at
synapses.
Channels or passive transport to allow hydrophilic particles across by acilitated
difusion.
Pumps or active transport which use ATP to move particles across the membrane.
 Table 1

B ecause o these varied unctions, membrane proteins are very diverse


in structure and in their position in the membrane. They can be divided
 Figure 8 Hormone receptor ( purple) into two groups.
embedded in phospholipid bilayer (grey) .
 Integral proteins are hydrophobic on at least part o their surace and
The hormone (blue/red) is thyroid
stimulating hormone. G-protein (brown) they are thereore embedded in the hydrocarbon chains in the centre
conveys the hormone's message to the o the membrane. Many integral proteins are transmembrane  they
interior o the cell extend across the membrane, with hydrophilic parts proj ecting
through the regions o phosphate heads on either side.

30
1 . 3 M e M b rAn e s tru ctu r e

 Peripheral proteins are hydrophilic on their surace, so are not


embedded in the membrane. Most o them are attached to the surace
o integral proteins and this attachment is oten reversible. Some have
a single hydrocarbon chain attached to them which is inserted into
the membrane, anchoring the protein to the membrane surace.
Figure 9 includes examples o both types o membrane protein.
Membranes all have an inner ace and an outer ace and membrane
proteins are orientated so that they can carry out their unction correctly.
For example, pump proteins in the plasma membranes o root cells in
plants are orientated so that they pick up potassium ions rom the soil
and pump them into the root cell.
The protein content o membranes is very variable, because the unction
o membranes varies. The more active a membrane, the higher is its
protein content. Membranes in the myelin sheath around nerve fbres
j ust act as insulators and have a protein content o only 1 8% .
The protein content o most plasma membranes on the outside o the
cell is about 5 0% . The highest protein contents are in the membranes o
chloroplasts and mitochondria, which are active in photosynthesis and
respiration. These have protein contents o about 75 % .

dawig mma 


Draw the fuid mosaic model o membrane structure.
The structure o membranes is ar too complicated The diagram shows these components o a
or us to show all o it in ull detail in a drawing, membrane:
but we can show our understanding o it using  phospholipids;
symbols to represent the molecules present.
A diagram o membrane structure is shown  integral proteins;
in fgure 9.  peripheral proteins;
 cholesterol.

 Figure 9 Membrane structure

31
1 C E LL B I O LO G Y

Identiy which each component in the diagram is.


Using similar symbols to represent the
components draw the structure o a membrane,
according to the fuid mosaic model, that contains
these proteins: channels or acilitated diusion,
pumps or active transport, immobilized enzymes
and receptors or hormones or neurotransmitters.
It is worth thinking about what you have been
doing when you draw the fuid mosaic model
o membrane structure. D rawings simpliy and
interpret a structure or process. They are used
in science as visual explanations. They show our
understanding o a structure or process and not
merely what it looks like. D rawings are based
on models, hypotheses or theories. For example,
when we show an animal tissue as a group o cells
with lines to represent the plasma membranes, we
are basing our drawing on the cell theory.
A diagram in a book or scientic paper usually
starts out as a drawing on paper by the author,
which is tidied up to make it suitable or printing.
It is now possible to use computer sotware,
but a pencil and paper are perhaps still the best
way to draw. No artistic ability is needed or
scientic drawing, and all biologists can develop
and improve their drawing skills. O  course some
 Figure 10 Anatomical drawings by Leonardo da Vinci
biologists produce particularly good drawings.
Some examples are shown in gure 1 0.

Cholesterol in membranes
Cholesterol is a component of animal cell membranes.
The two main components o cell membranes are phospholipids and
proteins. Animal cell membranes also contain cholesterol.
C holesterol is a type o lipid, but it is not a at or oil. Instead it belongs
CH 3 CH 2 CH 2 CH 3
to a group o substances called steroids. Most o a cholesterol molecule
cholesterol CH CH 2 CH is hydrophobic so it is attracted to the hydrophobic hydrocarbon
CH 3
CH 3 tails in the centre o the membrane, but one end o the cholesterol
molecule has a hydroxyl ( - O H) group which is hydrophilic. This is
CH 3
attracted to the phosphate heads on the periphery o the membrane.
C holesterol molecules are thereore positioned between phospholipids
in the membrane.
HO
hydrophilic hydrophobic The amount o cholesterol in animal cell membranes varies. In the
membranes o vesicles that hold neurotransmitters at synapses as much
 Figure 11 The structure of cholesterol
o 3 0% o the lipid in the membrane is cholesterol.

32
1 . 4 M e M b r An e trAn s Po r t

The role of cholesterol in membranes


Cholesterol in mammalian membranes reduces
membrane fuidity and permeability to some solutes.
C ell membranes do not correspond exactly to any o the three states
o matter. The hydrophobic hydrocarbon tails usually behave as a
liquid, but the hydrophilic phosphate heads act more like a solid.
O verall the membrane is fuid as components o the membrane are
ree to move.
The fuidity o animal cell membranes needs to be careully
controlled. I they were too fuid they would be less able to control
what substances pass through, but i they were not fuid enough the
movement o the cell and substances within it would be restricted.
C holesterol disrupts the regular packing o the hydrocarbon tails
o phospholipid molecules, so prevents them crystallizing and
behaving as a solid. However it also restricts molecular motion
and thereore the fuidity o the membrane. It also reduces the
permeability to hydrophilic particles such as sodium ions and
hydrogen ions. D ue to its shape cholesterol can help membranes
to curve into a concave shape, which helps in the ormation o
vesicles during endocytosis.

1.4 Mma ap


Understanding Applications
 Particles move across membranes by simple  Structure and unction o sodiumpotassium
diusion, acilitated diusion, osmosis and pumps or active transport and potassium
active transport. channels or acilitated diusion in axons.
 The fuidity o membranes allows materials to  Tissues or organs to be used in medical
be taken into cells by endocytosis or released procedures must be bathed in a solution with
by exocytosis. the same osmolarity as the cytoplasm to
 Vesicles move materials within cells. prevent osmosis.

Nature of science Skills


 Experimental design: accurate quantitative  Estimation o osmolarity in tissues by bathing
measurements in osmosis experiments samples in hypotonic and hypertonic solutions.
are essential.

33
1 C E LL B I O LO G Y

outside of cell endocytosis


Endocytosis
The fuidity o membranes allows materials to be taken
cell interior into cells by endocytosis or released by exocytosis.
A vesicle is a small sac o membrane with a droplet o fuid inside.
Vesicles are spherical and are normally present in eukaryotic cells.
They are a very dynamic eature o cells. They are constructed, moved
around and then deconstructed. This can happen because o the fuidity
o membranes, which allows structures surrounded by a membrane to
change shape and move.
To orm a vesicle, a small region o a membrane is pulled rom the rest
o the membrane and is pinched o. Proteins in the membrane carry out
this process, using energy rom ATP.
Vesicles can be ormed by pinching o a small piece o the plasma
membrane o cells. The vesicle is ormed on the inside o the plasma
membrane. It contains material that was outside the cell, so this is a
method o taking materials into the cell. It is called endocytosis.
Figure 1 shows how the process occurs.
Vesicles taken in by endocytosis contain water and solutes rom
outside the cell but they also oten contain larger molecules needed
by the cell that cannot pass across the plasma membrane. For
example, in the placenta, proteins rom the mothers blood,
including antibodies, are absorbed into the etus by endocytosis.
vesicle S ome cells take in large undigested ood particles by endocytosis. This
happens in unicellular organisms including Amoeba and Paramecium.
S ome types o white blood cells take in pathogens including bacteria
and viruses by endocytosis and then kill them, as part o the bodys
 Figure 1 Endocytosis response to inection.

Vesicle movement in cells


Vesicles move materials within cells.
Vesicles can be used to move materials around inside cells. In some
cases it is the contents o the vesicle that need to be moved. In other
cases it is proteins in the membrane o the vesicle that are the reason or
vesicle movement.
An example o moving the vesicle contents occurs in secretory
cells. Protein is synthesized by ribosomes on the rough endoplasmic
reticulum ( rE R) and accumulates inside the rE R. Vesicles containing
the proteins bud o the rE R and carry them to the Golgi apparatus.
The vesicles use with the Golgi apparatus, which processes the
protein into its nal orm. When this has been done, vesicles bud o
the Golgi apparatus and move to the plasma membrane, where the
protein is secreted.
In a growing cell, the area o the plasma membrane needs to increase.
Phospholipids are synthesized next to the rER and become inserted
into the rER membrane. Ribosomes on the rER synthesize membrane
proteins which also become inserted into the membrane. Vesicles bud
o the rE R and move to the plasma membrane. They use with it, each

34
1 . 4 M e M b r An e trAn s Po r t

increasing the area of the plasma membrane by a very small amount. outside of cell
This method can also be used to increase the size of organelles in the
exocytosis
cytoplasm such as lysosomes and mitochondria.
Vesicles bud o from
Proteins are synthesized Vesicles bud o from The Golgi the Golgi apparatus
by ribosomes and then enter the rER and carry the apparatus and carry the modied vesicle
the rough endoplasmic proteins to the Golgi modies the proteins to the plasma
reticulum apparatus proteins membrane

ENDOCYTOSIS EXOCYTOSIS
Part of the plasma Vesicles fuse
membrane is pulled inwards with the plasma
A droplet of uid becomes membrane
enclosed when a vesicle is The contents of
pinched o the vesicle are
Vesicles can then move expelled
through the cytoplasm The membrane
carrying their contents then attens
out again
 Figure 2

Exocytosis
The fuidity o membranes allows materials to be taken
into cells by endocytosis or released by exocytosis.
Vesicles can be used to release materials from cells. If a vesicle fuses with
the plasma membrane, the contents are then outside the membrane and
therefore outside the cell. This process is called exocytosis.
D igestive enzymes are released from gland cells by exocytosis. The
polypeptides in the enzymes are synthesized by the rER, processed in
the Golgi apparatus and then carried to the membrane in vesicles for cell interior
exocytosis. In this case the release is referred to as secretion, because a
 Figure 3 Exocytosis
useful substance is being released, not a waste product.
E xocytosis can also be used to expel waste products or unwanted
materials. An example is the removal of excess water from the cells of
unicellular organisms. The water is loaded into a vesicle, sometimes
called a contractile vacuole, which is then moved to the plasma
membrane for expulsion by exocytosis. This can be seen quite easily in
contractile
Paramecium, using a microscope. Figure 4 shows a drawing of Paramecium vesicle
showing a contractile vesicle at each end of the cell.

Simple difusion mouth

Particles move across membranes by simple diusion,


acilitated diusion, osmosis and active transport. endoplastule
S imple diffusion is one of the four methods of moving particles
across membranes.
endoplast
D iffusion is the spreading out of particles in liquids and gases that
happens because the particles are in continuous random motion. contractile
More particles move from an area of higher concentration to an vesicle
area of lower concentration than move in the opposite direction.
There is therefore a net movement from the higher to the lower
concentration  a movement down the concentration gradient. Living  Figure 4 Drawing of Paramecium

35
1 C E LL B I O LO G Y

organisms do not have to use energy to make diusion occur so it is a


toK passive process.
can he same aa jusify S imple diusion across membranes involves particles passing
muually exlusive between the phospholipids in the membrane. It can only happen
nlusins? i the phospholipid bilayer is permeable to the particles. Non- polar
In an experiment to test particles such as oxygen can diuse through easily. I the oxygen
whether NaCl can difuse concentration inside a cell is reduced due to aerobic respiration and
through dialysis tubing, a the concentration outside is higher, oxygen will pass into the cell
1% solution o NaCl was through the plasma membrane by passive diusion. An example is
placed inside a dialysis tube shown in fgure 6 .
and the tube was clamped
shut. The tube containing
the solution was immersed
in a beaker containing
water. A conductivity meter
was inserted into the water
surrounding the tubing. I the
conductivity o the solution  Figure 5 Model o difusion with dots representing particles
increases, then the NaCl is
The centre o membranes is hydrophobic, so ions with positive or negative
difusing out o the tubing.
charges cannot easily pass through. Polar molecules, which have partial
positive and negative charges over their surace, can diuse at low rates
time /s  1 cnuiviy
between the phospholipids o the membrane. Small polar particles such as
 10 mg l - 1
urea or ethanol pass through more easily than large particles.
0 81.442
30 84.803 the cornea has no blood supply so its cells obtain
60 88.681 oxygen by simple diusion from the air
90 95.403 high concentration
120 99.799 of oxygen in the air
air
high concentration
uid (tears)
Noting the uncertainty o the of oxygen in the tears
cell on outer that coat the cornea
conductivity probe, discuss surface of the
whether the data supports cornea
the conclusion that NaCl is
difusing out o the dialysis oxygen passes through lower concentration
tubing. the plasma membrane by of oxygen in the cornea
simple diusion cells due to aerobic respiration
 Figure 6 Passive difusion

daa-base quesins:
Difusion o oxygen in the cornea 1 C alculate the thickness o the rabbit cornea in
Oxygen concentrations were measured in the millimetres. [1 ]
cornea o anesthetized rabbits at dierent distances 2 a) D escribe the trend in oxygen
rom the outer surace. These measurements were concentrations in the cornea rom the
continued into the aqueous humor behind the outer to the inner surace. [2 ]
cornea. The rabbits cornea is 400 micrometres
(400 m) thick. The graph (fgure 7) shows the b) Suggest reasons or the trend in oxygen
measurements. You may need to look at a diagram concentration in the cornea. [2 ]
o eye structure beore answering the questions. 3 a) C ompare the oxygen concentrations in
The oxygen concentration in normal air is the aqueous humor with the
2 0 kilopascals ( 2 0 kPa) . concentrations in the cornea. [2 ]

36
1 . 4 M e M b r An e trAn s Po r t

b) Using the data in the graph, deduce 20


whether oxygen diffuses from the
cornea to the aqueous humor. [2 ]
4 Using the data in the graph, evaluate diffusion

Concentration of oxygen/kPa
15
as a method of moving substances in large
multicellular organisms. [2 ]
5 a) Predict the effect of wearing contact 10
lenses on oxygen concentrations in
the cornea. [1 ]
b) S uggest how this effect could be
5
minimized. [1 ]
6 The range bars for each data point indicate
how much the measurements varied.
0
Explain the reason for showing range 0 100 200 300 400
bars on the graph. [2 ] distance from outer surface of cornea/m
 Figure 7

Facilitated difusion
Particles move across membranes by simple difusion,
acilitated difusion, osmosis and active transport.
Facilitated diffusion is one of the four methods of moving particles
across membranes.
Ions and other particles that cannot diffuse between phospholipids
can pass into or out of cells if there are channels for them through
the plasma membrane. These channels are holes with a very narrow
diameter. The walls of the channel consist of protein. The diameter (a)
and chemical properties of the channel ensure that only one type of
particle passes through, for example sodium ions, or potassium ions,
but not both.
B ecause these channels help particles to pass through the membrane,
from a higher concentration to a lower concentration, the process is
called facilitated diffusion. C ells can control which types of channel
are synthesized and placed in the plasma membrane and in this way
they can control which substances diffuse in and out.
(b)
Figure 8 shows the structure of a channel for magnesium ions,
viewed from the side and from the outside of the membrane. The
Membrane
structure of the protein making up the channel ensures that only
magnesium ions are able to pass through the hole in the centre. Cytoplasm

Osmosis
Particles move across membranes by simple difusion,
acilitated difusion, osmosis and active transport.
Osmosis is one of the four methods of moving particles across
membranes.  Figure 8 Magnesium channel

37
1 C E LL B I O LO G Y

Water is able to move in and out o most cells reely.


S ometimes the number o water molecules moving
in and out is the same and there is no net movement,
but at other times more molecules move in one
direction or the other. This net movement is osmosis.
O smosis is due to dierences in the concentration o
substances dissolved in water ( solutes) . Substances
dissolve by orming intermolecular bonds with
 Figure 9 water molecules. These bonds restrict the movement
o the water molecules. Regions with a higher solute concentration
thereore have a lower concentration o water molecules ree to move
than regions with a lower solute concentration. B ecause o this there
is a net movement o water rom regions o lower solute concentration
to regions with higher solute concentration. This movement is passive
because no energy has to be expended directly to make it occur.
O smosis can happen in all cells because water molecules, despite being
hydrophilic, are small enough to pass though the phospholipid bilayer.
Some cells have water channels called aquaporins, which greatly
increase membrane permeability to water. E xamples are kidney cells that
reabsorb water and root hair cells that absorb water rom the soil.
At its narrowest point, the channel in an aquaporin is only slightly wider than
water molecules, which thereore pass through in single fle. Positive charges
at this point in the channel prevent protons (H+ ) rom passing through.

Active transport
Particles move across membranes by simple difusion,
acilitated difusion, osmosis and active transport.
Active transport is one o the our methods o moving particles across
membranes.
C ells sometimes take in substances, even though there is already a
higher concentration inside than outside. The substance is absorbed
against the concentration gradient. Less commonly, cells sometimes
pump substances out, even though there is already a larger
concentration outside.
This type o movement across membranes is not diusion and energy is
needed to carry it out. It is thereore called active transport. Most active
transport uses a substance called ATP as the energy supply or this
process. E very cell produces its own supply o ATP by cell respiration.
Active transport is carried out by globular proteins in membranes,
usually called pump proteins. The membranes o cells contain many
dierent pump proteins allowing the cell to control the content o its
cytoplasm precisely.
Figure 1 0 illustrates how a pump protein works. The molecule or ion
enters the pump protein and can reach as ar as a central chamber. A
conormational change to the protein takes place using energy rom
ATP. Ater this, the ion or molecule can pass to the opposite side o the
membrane and the pump protein returns to its original conormation.
 Figure 10 Action of a pump protein The pump protein shown transports Vitamin B 1 2 into E. coli.

38
1 . 4 M e M b r An e trAn s Po r t

daa-a qui: Phosphate absorption in barley roots oxyg nig Phpha


/% /% api/ml
Roots were cut off from barley plants and were used to investigate
g1 h 1
phosphate absorption. Roots were placed in phosphate solutions and
0.1 99.9 0.07
air was bubbled through. The phosphate concentration was the same
in each case, but the percentage of oxygen and nitrogen was varied 0.3 99.7 0.15
in the air bubbled through. The rate of phosphate absorption was 0.9 99.1 0.27
measured. Table 1 shows the results. 2.1 97.1 0.32
1 Describe the effect of reducing the oxygen concentration below 21 .0% 21.0 79.0 0.33
on the rate of phosphate absorption by roots. You should only use  Table 1
information from the table in your answer. [3 ] 0 .4

2 Explain the effect of reducing the oxygen percentage from 0 .3

2 1 .0 to 0.1 on phosphate absorption. In your answer you Phosphate 0 .2


should use as much biological understanding as possible of absorption
how cells absorb mineral ions. [3 ] /mol g2 1 h 2 1 0 .1

An experiment was done to test which method of membrane 0


0 2 4 6 8 10
transport was used by the roots to absorb phosphate. Roots were DNP concentration / mmol dm 2 3
placed in the phosphate solution as before, with 2 1 .0% oxygen  Figure 11 Efect o DNP concentration
bubbling through. Varying concentrations of a substance called on phosphate absorption
D NP were added. D NP blocks the production of ATP by aerobic cell
respiration. Figure 1 1 shows the results of the experiment.
3 D educe, with a reason, whether the roots absorbed the
phosphate by diffusion or active transport. [2 ]
4 D iscuss the conclusions that can be drawn from the data in
the graph about the method of membrane transport used by
the roots to absorb phosphate. [2 ]

Active transport of sodium and potassium in axons


Structure and function of sodiumpotassium pumps for active transport.
An axon is part of a neuron ( nerve cell) and The sodiumpotassium pump follows a repeating
consists of a tubular membrane with cytoplasm cycle of steps that result in three sodium ions
inside. Axons can be as narrow as one micrometre being pumped out of the axon and two potassium
in diameter, but as long as one metre. Their ions being pumped in. Each time the pump goes
function is to convey messages rapidly from one round this cycle it uses one ATP. The cycle consists
part of the body to another in an electrical form of these steps:
called a nerve impulse.
1 The interior of the pump is open to the inside
A nerve impulse involves rapid movements of of the axon; three sodium ions enter the
sodium and then potassium ions across the axon pump and attach to their binding sites.
membrane. These movements occur by facilitated
2 ATP transfers a phosphate group from itself
diffusion through sodium and potassium
to the pump; this causes the pump to change
channels. They occur because of concentration
shape and the interior is then closed.
gradients between the inside and outside of the
axon. The concentration gradients are built up 3 The interior of the pump opens to the
by active transport, carried out by a sodium outside of the axon and the three sodium
potassium pump protein. ions are released.

39
1 C E LL B I O LO G Y

4 Two potassium ions from outside can then 6 The interior of the pump opens to the inside
enter and attach to their binding sites. of the axon and the two potassium ions are
released; sodium ions can then enter and bind
5 B inding of potassium causes release of the
to the pump again ( stage 1 ) .
phosphate group; this causes the pump to
change shape again so that it is again only
open to the inside of the axon.

1 2 3

p p
ATP
ADP

4 5 6

p
p

 Figure 12 Active transport in axons

Facilitated difusion o potassium in axons


Structure and unction o sodiumpotassium pumps or active transport and
potassium channels or acilitated difusion in axons.
A nerve impulse involves rapid movements of Potassium ions are slightly smaller than 0 . 3 nm,
sodium and then potassium ions across the axon but when they dissolve they become bonded
membrane. These movements occur by facilitated to a shell of water molecules that makes them
diffusion through sodium and potassium too large to pass through the pore. To pass
channels. Potassium channels will be described through, the bonds between the potassium
here as a special example of facilitated diffusion. ion and the surrounding water molecules are
E ach potassium channel consists of four protein broken and bonds form temporarily between
subunits with a narrow pore between them that the ion and a series of amino acids in the
allows potassium ions to pass in either direction. narrowest part of the pore. After the potassium
The pore is 0.3 nm wide at its narrowest. ion has passed through this part of the pore,

40
1 . 4 M e M b r An e trAn s Po r t

it can again become associated with a shell o positive charges outside than inside, potassium
water molecules. channels are closed. At one stage during a nerve
impulse there are relatively more positive charges
Other positively charged ions that we might expect
inside. This causes potassium channels to open,
to pass through the pore are either too large to t
allowing potassium ions to diuse through.
through or are too small to orm bonds with the
However, the channel rapidly closes again. This
amino acids in the narrowest part o the pore, so
seems to be due to an extra globular protein
they cannot shed their shell o water molecules.
subunit or ball, attached by a fexible chain o
This explains the specicity o the pump.
amino acids. The ball can t inside the open
Potassium channels in axons are voltage gated. pore, which it does within milliseconds o the
Voltages across membranes are due to an pore opening. The ball remains in place until the
imbalance o positive and negative charges across potassium channel returns to its original closed
the membrane. I an axon has relatively more state. This is shown in gure 1 3 .

1 channel closed 2 channel briey open net negative charge

+ + + + + + + + - - - - - - - - outside
+ +
+ +
+ +
+ +

++ + + +
+++
- - - - - - - - - + + + + + + + inside of axon
chain
net negative charge inside
K+ ions net positive
ball the axon and net positive
charge
charge outside

3 channel closed by ball and chain


- - - - - - - -
+ +
+ +
+ +
+ +

+ + + + + + + +
hydrophobic core hydrophilic outer
of the membrane parts of the membrane

 Figure 13

eimai f mlaiy
Estimation of osmolarity in tissues by bathing samples in hypotonic and
hypertonic solutions.
O smosis is due to solutes that orm bonds with units or measuring it are osmoles or milliosmoles
water. These solutes are osmotically active. ( mO sm) . The normal osmolarity o human tissue
Glucose, sodium ions, potassium ions and chloride is about 3 00 mO sm.
ions are all osmotically active and solutions o
An isotonic solution has the same osmolarity
them are oten used in osmosis experiments. C ells
as a tissue. A hypertonic solution has a higher
contain many dierent osmotically active solutes.
osmolarity and a hypotonic solution has a lower
The osmolarity o a solution is the total osmolarity. I samples o a tissue are bathed
concentration o osmotically active solutes. The in hypertonic and hypotonic solutions, and

41
1 C E LL B I O LO G Y

measurements are taken to fnd out whether isotonic and thereore fnd out the osmolarity o
water enters or leaves the tissue, it is possible to the tissue. The data- based questions below give
deduce what concentration o solution would be the results rom an experiment o this type.

data-base questions: Osmosis in 4 Explain the reasons or using percentage


plant tissues mass change rather than the actual
I samples o plant tissue are bathed in salt or mass change in grams in this type o
sugar solutions or a short time, any increase experiment. [2 ]
or decrease in mass is due almost entirely to
40
water entering or leaving the cells by osmosis. + + +
+ +
Figure 1 4 shows the percentage mass change 30
+ + + +
o our tissues, when they were bathed in salt PINE
KERNEL
solutions o dierent concentrations. 20

Sodium chloride
1 a) S tate whether water moved into or out 10
concentration
o the tissues at 0.0 mol dm 3 sodium % / mol dm 2 3
0
chloride solution. [1 ] Mass 0 .1 0 .2 0 .3 0 .4 0 .5 0 .6 0 .7 0 .8 0 .9 1.0

change
b) State whether water moved into or out 2 10 BUTTERNUT
SQUASH
o the tissues at 1 .0 mol dm 3 sodium 2 20 SWEET
chloride solution. [2 ] POTATO
2 30
2 D educe which tissue had the lowest solute
concentration in its cytoplasm. Include 2 40

how you reached your conclusion in


2 50 CACTUS
your answer. [2 ]
3 S uggest reasons or the dierences in solute  Figure 14 Mass changes in plant tissues bathed in
concentration between the tissues. [3 ] salt solutions

The experiment in the data- based question can 5 Leave the tissue in the solutions or long
be repeated using potato tubers, or any other enough to get a signifcant mass change, but
plant tissue rom around the world that is not so long that another actor aects the
homogeneous and tough enough to be handled mass, such as decomposition!
without disintegrating.
6 You might choose to be more inventive
D iscuss with a partner or group how you could do in your experimental approach. Figure 1 5
the ollowing things: gives one idea or measuring changes to the
turgidity o plant tissue, but other methods
1 D ilute a 1 mol dm 3 sodium chloride
could be used.
solution to obtain the concentrations shown
on the graph.
2 O btain samples o a plant tissue that
are similar enough to each other to give 
angle gives
comparable results. measure
plant tissue of turgidity
3 Ensure that the surace o the tissue samples is
dry when fnding their mass, both at the start
and end o the experiment.
weight
4 Ensure that all variables are kept constant,
apart rom salt concentration o the  Figure 15 Method of assessing turgidity
bathing solution. of plant tissue

42
1 . 4 M e M b r An e trAn s Po r t

expimal dig
Experimental design: accurate quantitative
measurements in osmosis experiments are essential.
An ideal experiment gives results that have only one reasonable
interpretation. C onclusions can be drawn from the results without any
doubts or uncertainties. In most experiments there are some doubts
and uncertainties, but if the design of an experiment is rigorous, these
can be minimized. The experiment then provides strong evidence for
or against a hypothesis.
This checklist can be used when designing an experiment:
 Results should if possible be quantitative as these give stronger
evidence than descriptive results.
 Measurements should be as accurate as possible, using the most
appropriate and best quality meters or other apparatus.
 Repeats are needed, because however accurately quantitative
measurements are taken biological samples are variable.
 All factors that might affect the results of the experiment must be
controlled, with only the factors under investigation being allowed
to vary and all other factors remaining constant.  Figure 16 Replicates are needed for each
treatment in a rigorous experiment
After doing an experiment the design can be evaluated using this
checklist. The evaluation might lead to improvements to the design
that would have made the experiment more rigorous.
If you have done an osmosis experiment in which samples of plant
tissue are bathed in solutions of varying solute concentration, you
can evaluate its design. If you did repeats for each concentration of
solution, and the results were very similar to each other, your results
were probably reliable.

Designing osmosis experiments


Rigorous experimental design is needed to produce
reliable results: how can accurate quantitative
measurements be obtained in osmosis experiments?
The osmolarity of plant tissues can be investigated in many ways.
Figure 1 7 shows some red onion cells that had been placed in a
sodium chloride solution. The following method can be used to
observe the consequences of osmosis in red onion cells.
1 Peel off some epidermis from the scale of a red onion bulb.
2 C ut out a sample of it, about 5  5 mm.
3 Mount the sample in a drop of distilled water on a microscope
slide, with a cover slip.  Figure 17 Micrograph of red onion cells placed
in salt solution

43
1 C E LL B I O LO G Y

4 O bserve using a microscope. The cytoplasm should fll the space


inside the cell wall, with the plasma membrane pushed up against it.
5 Mount another sample o epidermis in sodium chloride solutions
with concentration o 0.5 mol dm - 3 or 3 % . I water leaves the cells
by osmosis and the volume o cytoplasm is reduced, the plasma
membrane pulls away rom the cell wall, as shown in Figure 1 7.
Plant cells with their membranes pulled away rom their cell walls
are plasmolysed and the process is plasmolysis.
This method can be used to help design an experiment to fnd out the
osmolarity o onion cells or other cells in which the area occupied by
the cytoplasm can easily be seen. The checklist in the previous section
can be used to try to ensure that the design is rigorous.

Preventing osmosis in excised tissues and organs


Tissues or organs to be used in medical procedures must be bathed in a solution
with the same osmolarity as the cytoplasm to prevent osmosis.
Animal cells can be damaged by osmosis. bathed in solutions with ( a) the same osmolarity,
Figure 1 8 shows blood cells that have been ( b) higher osmolarity and ( c) lower osmolarity.
a) b) c)

 Figure 18 Blood cells bathed in solutions o diferent solute concentration


In a solution with higher osmolarity ( a hypertonic used, which is called normal saline. It has an
solution) , water leaves the cells by osmosis so osmolarity o about 3 00 mO sm ( milliO smoles) .
their cytoplasm shrinks in volume. The area
Normal saline is used in many medical
o plasma membrane does not change, so it
procedures. It can be:
develops indentations, which are sometimes called
crenellations. In a solution with lower osmolarity  saely introduced to a patients blood system
( hypotonic) , the cells take in water by osmosis via an intravenous drip.
and swell up. They may eventually burst, leaving  used to rinse wounds and skin abrasions.
ruptured plasma membranes called red cell ghosts.
 used to keep areas o damaged skin moistened
B oth hypertonic and hypotonic solutions thereore prior to skin grats.
damage human cells, but in a solution with same
osmolarity as the cells ( isotonic) , water molecules  used as the basis or eye drops.
enter and leave the cells at the same rate so they  rozen to the consistency o slush or packing
remain healthy. It is thereore important or hearts, kidneys and other donor organs that
any human tissues and organs to be bathed in have to be transported to the hospital where
an isotonic solution during medical procedures. the transplant operation is to be done.
Usually an isotonic sodium chloride solution is

44
1 . 5 tH e o rI GI n o f ce lls

 Figure 19 Donor liver packed in an isotonic medium, surrounded by isotonic slush. There is a worldwide shortage of donor
organs  in most countries it is possible to register as a possible future donor

1.5 th igi  


Understanding Applications
 Cells can only be ormed by division o
 Evidence rom Pasteurs experiments that
pre-existing cells. spontaneous generation o cells and organisms
 The frst cells must have arisen rom does not now occur on Earth.
non-living material.
 The origin o eukaryotic cells can be explained
by the endosymbiotic theory. Nature of science
 Testing the general principles that underlie the
natural world: the principle that cells only come
rom pre-existing cells needs to be verifed.

Cell division and the origin of cells


Cells can only be ormed by division o pre-existing cells.
Since the 1 880s there has been a theory in biology that cells can only be
produced by division of a pre-existing cell. The evidence for this hypothesis
is very strong and is discussed in the nature of science panel below.
The implications of the hypothesis are remarkable. If we consider the
trillions of cells in our bodies, each one was formed when a previously

45
1 C E LL B I O LO G Y

existing cell divided in two. B eore that all o the genetic material in
toK
the nucleus was copied so that both cells ormed by cell division had a
Wha d we gain, and wha d we le, nucleus with a ull complement o genes. We can trace the origin o cells
when we name mehing? in the body back to the frst cell  the zygote that was the start o our
lives, produced by the usion o a sperm and an egg.
When Dr Craig Venters team
announced that they had succeeded S perm and egg cells were produced by cell division in our parents. We
in transplanting the synthetic genome can trace the origins o all cells in our parents bodies back to the zygote
rom one bacterium into another rom which they developed, and then continue this process over the
bacterium in the journal Science some generations o our human ancestors. I we accept that humans evolved
ethicists responded by questioning rom pre- existing ancestral species, we can trace the origins o cells back
the language o calling it the creation through hundreds o millions o years to the earliest cells on Earth.
o a synthetic cell: There is thereore a continuity o lie rom its origins on Earth to the cells
in our bodies today.
The science is ying 30,000 eet over
the publics understanding ... Scientists In 2 01 0 there were reports that biologists had created the frst artifcial
can be their own worst enemy by using cell, but this cell was not entirely new. The base sequence o the D NA
words like clone or synthetic lie. o a bacterium ( Mycoplasma mycoides) was synthesized artifcially, with a
ew deliberate changes. This D NA was transerred to pre- existing cells
Glenn Mcgee, funde f Ameican
o a dierent type o bacterium ( Mycoplasma capricolum) , which was
Junal f biehic
eectively converted into Mycoplasma mycoides. This process was thereore
Frankly, hes describing it in a way an extreme orm o genetic modifcation and the creation o entirely
thats drumming up controversy more new cells remains an insuperable challenge at the moment.
than characterising it accurately. His
claim that weve got the frst sel-
replicating lie orm whose parent is a Aciviy
computer, thats just silly.
the l f silphium
It misuses the word parent. The
advance here needs to be described The Greek coin in fgure 2 depicts a Silphium plant, which grew in a small part
in sane and accurate ways. What o what is now Libya and was highly prized or its medicinal uses, especially
he's managed to do is synthesise a as a birth control agent. It seems to have been so widely collected that within a
genome much larger than any genome ew hundred years o the ancient Greeks colonizing North Arica it had become
thats been synthesised rom scratch extinct. Rather than arising again spontaneously, Silphium has remained extinct
beore. and we cannot now test its contraceptive properties scientifcally. How can we
prevent the loss o other plants that could be o use to us?
Gegy Kaenick, Haing Iniue
reeach schla

 Figure 2 An ancient Greek coin, showing Silphium


 Figure 1 Synthetic Mycoplasma bacteria

46
1 . 5 tH e o rI GI n o f ce lls

Spontaneous generation and the origin of cells


Veriying the general principles that underlie the natural world: the principle that
cells only come rom pre-existing cells needs to be verifed.
Spontaneous generation is the ormation o living S ome biologists remained convinced that
organisms rom non-living matter. The Greek spontaneous generation could occur i there
philosopher and botanist Theophrastus reported was access to the air. Louis Pasteur responded
that a plant called Silphium had sprung up rom soil by carrying out careully designed experiments
where it was not previously present and described with swan- necked fasks, which established
this as an example o spontaneous generation. beyond reasonable doubt that spontaneous
Aristotle wrote about insects being ormed rom generation o lie does not now occur. Pasteurs
the dew alling on leaves or rom the hair, fesh or experiments are described in the next section o
aeces o animals. In the 1 6th century the German- this sub- topic.
Swiss botanist and astrologer Paracelsus quoted
Apart rom the evidence rom the experiments
observations o spontaneous generation o mice,
o Pasteur and others, there are other reasons
rogs and eels rom water, air or decaying matter.
or biologists universally accepting that cells only
It is easy to see how ideas o spontaneous come rom pre- existing cells:
generation could have persisted when cells and  A cell is a highly complex structure and no
microorganisms had not been discovered and the
natural mechanism has been suggested or
nature o sexual reproduction was not understood.
producing cells rom simpler subunits.
From the 1 7th century onwards biologists carried
out experiments to test the theory that lie could  No example is known o increases in the
arise rom non-living matter. Francesco Redi number o cells in a population, organism or
showed that maggots only developed in rotting tissue without cell division occurring.
meat i fies were allowed to come into contact  Viruses are produced rom simpler subunits
with it. Lazzaro Spallanzani boiled soup in eight but they do not consist o cells, and they can
containers, then sealed our o them and let the only be produced inside the host cells that
others open to the air. Organisms grew in the they have inected.
containers let open but not in the others.

Spontaneous generation and Pasteurs experiments


Evidence rom Pasteurs experiments that spontaneous generation o cells and
organisms does not now occur on Earth.
Louis Pasteur made a nutrient broth by boiling then melted the glass o the necks and bent it into
water containing yeast and sugar. He showed that a variety o shapes, shown in gure 3 .
i this broth was kept in a sealed fask, it remained
Pasteur then boiled the broth in some o the
unchanged, and no ungi or other organisms
fasks to kill any organisms present but let others
appeared. He then passed air though a pad o
unboiled as controls. Fungi and other organisms
cotton wool in a tube, to lter out microscopic
soon appeared in the unboiled fasks but not in
particles rom the air, including bacteria and the
the boiled ones, even ater long periods o time.
spores o ungi. I the pad o cotton wool was
The broth in the fasks was in contact with air,
placed in broth in a sealed fask, within 3 6 hours,
which it had been suggested was needed or
there were large number o microorganisms in
spontaneous generation, yet no spontaneous
the broth and mould grew over its surace.
generation occurred. Pasteur snapped the necks o
The most amous o Pasteurs experiments some o the fasks to leave a shorter vertical neck.
involved the use o swan-necked fasks. He placed Organisms were soon apparent in these fasks and
samples o broth in fasks with long necks and decomposed the broth.

47
1 C E LL B I O LO G Y

Pasteur published his results in 1 860 and rom the air getting into the broth or other liquids
subsequently repeated them with other liquids and that no organisms appeared spontaneously. His
including urine and milk, with the same results. He experiments convinced most biologists, both at the
concluded that the swan necks prevented organisms time o publication and since then.

Origin o the frst cells


The frst cells must have arisen rom non-living material.
I we trace back the ancestry o cells over billions o years, we must
eventually reach the earliest cells to have existed. These were the frst
living things on Earth. Unless cells arrived on E arth rom somewhere
else in the universe, they must have arisen rom non- living material.
This is a logical conclusion, but it gives perhaps the hardest question o
all or biologists to answer: how could a structure as complex as the cell
have arisen by natural means rom non-living material?
It has sometimes been argued that complex structures cannot arise by
evolution, but there is evidence that this can happen in a series o stages
 Figure 3
Drawings o Pasteurs over long periods o time. Living cells may have evolved over hundreds
swan-necked fasks o millions o years. There are hypotheses or how some o the main
stages could have occurred.

1. Production of carbon compounds such as 2. Assembly of carbon compounds into


sugars and amino acids polymers
S tanley Miller and Harold Urey passed steam A possible site or the origin o the frst carbon
through a mixture o methane, hydrogen and compounds is around deep- sea vents. These are
ammonia. The mixture was thought to be cracks in the Earths surace, characterized by
representative o the atmosphere o the early gushing hot water carrying reduced inorganic
E arth. E lectrical discharges were used to simulate chemicals such as iron sulphide. These chemicals
lightning. They ound that amino acids and other represent readily accessible supplies o energy, a
carbon compounds needed or lie were produced. source o energy or the assembly o these carbon
compounds into polymers.
ammonia
water vapour (NH 3 )
methane (CH 4) electrode
hydrogen
(H 2 )

condenser

cold
water in

cooled water containing


organic compounds
 Figure 5 Deep sea vents

sample taken for


chemical analysis
 Figure 4 Miller and Ureys apparatus

48
1 . 5 tH e o rI GI n o f ce lls

3. Formation of membranes 4. Development of a mechanism for


I phospholipids or other amphipathic carbon inheritance
compounds were among the frst carbon Living organisms currently have genes made o
compounds, they would have naturally assembled D NA and use enzymes as catalysts. To replicate
into bilayers. Experiments have shown that these D NA and be able to pass genes on to ospring,
bilayers readily orm vesicles resembling the enzymes are needed. However, or enzymes to
plasma membrane o a small cell. This would have be made, genes are needed. The solution to this
allowed dierent internal chemistry rom that o conundrum may have been an earlier phase in
the surroundings to develop. evolution when RNA was the genetic material.
It can store inormation in the same way as
D NA but it is both sel- replicating and can itsel
act as a catalyst.

 Figure 6 Liposomes

Endosymbiosis and eukaryotic cells


The origin o eukaryotic cells can be explained by the
endosymbiotic theory.
The theory o endosymbiosis helps to explain the evolution o
eukaryotic cells. It states that mitochondria were once ree- living
prokaryotic organisms that had developed the process o aerobic cell
respiration. Larger prokaryotes that could only respire anaerobically
took them in by endocytosis. Instead o killing and digesting the Aiviy
smaller prokaryotes they allowed them to continue to live in their Wh did i bgi?
cytoplasm. As long as the smaller prokaryotes grew and divided as ast Erasmus Darwin was
as the larger ones, they could persist indefnitely inside the larger cells. Charles Darwins
According to the theory o endosymbiosis they have persisted over grandather. In a poem
hundreds o millions o years o evolution to become the mitochondria entitled The Temple o
inside eukaryotic cells today. Nature, published in 1803,
The larger prokaryotes and the smaller aerobically respiring ones were he tells us how and where
in a symbiotic relationship in which both o them benefted. This is he believed lie to have
known as a mutualistic relationship. The smaller cell would have been originated:
supplied with ood by the larger one. The smaller cell would have Organic Lie began
carried out aerobic respiration to supply energy efciently to the larger beneath the waves ...
cell. Natural selection thereore avoured cells that had developed this Hence without parent by
endosymbiotic relationship. spontaneous birth
The endosymbiotic theory also explains the origin o chloroplasts. Rise the frst specks o
I a prokaryote that had developed photosynthesis was taken in by animated earth
a larger cell and was allowed to survive, grow and divide, it could Has Erasmus Darwins
have developed into the chloroplasts o photosynthetic eukaryotes. hypothesis that lie began in
Again, both o the organisms in the endosymbiotic relationship would the sea been alsifed?
have benefted.

49
1 C E LL B I O LO G Y

original ancestral
Activity prokaryote evolution of the
nucleus
Bangiomorpha and the
origins of sex.
The frst known eukaryote evolution of
photosynthesis evolution of
and frst known evolution of linear chromosomes,
multicellular organism is aerobic respiration mitosis and meiosis
Bangiomorpha pubescens.
Fossils o this red alga
were discovered in 1,200
million year old rocks
rom northern Canada. It is
the frst organism known endocytosis produces
mitochondria
to produce two dierent
types o gamete a larger endocytosis
sessile emale gamete to produce
chloroplasts
and a smaller motile male
gamete. Bangiomorpha is
thereore the frst organism
known to reproduce
sexually. It seems unlikely evolution of evolution of
that eukaryote cell plant cells animal cells
structure, multicellularity
and sexual reproduction
evolved simultaneously.
What is the most likely
sequence or these
landmarks in evolution? plant cell animal cell
(eukaryotic) (eukaryotic)
 Figure 7 Endosymbiosis

Although no longer capable of living independently, chloroplasts


and mitochondria both have features that suggest they evolved from
independent prokaryotes:
 They have their own genes, on a circular D NA molecule like that of
prokaryotes.
 They have their own 70S ribosomes of a size and shape typical of
some prokaryotes.
 They transcribe their D NA and use the mRNA to synthesize some of
their own proteins.
 They can only be produced by division of pre- existing mitochondria
and chloroplasts.

50
1 . 6 ce ll d I VI s I o n

1.6 c ivii


Understanding Applications
 Mitosis is division o the nucleus into two
 The correlation between smoking and incidence
genetically identical daughter nuclei. o cancers.
 Chromosomes condense by supercoiling
during mitosis.
 Cytokinesis occurs ater mitosis and is dierent Skills
in plant and animal cells.  Identifcation o phases o mitosis in cells
 Interphase is a very active phase o the cell viewed with a microscope.
cycle with many processes occurring in the  Determination o a mitotic index rom a
nucleus and cytoplasm. micrograph.
 Cyclins are involved in the control o the
cell cycle.
 Mutagens, oncogenes and metastasis are Nature of science
involved in the development o primary and  Serendipity and scientifc discoveries: the
secondary tumours. discovery o cyclins was accidental.

The role of mitosis


Mitosis is division o the nucleus into two genetically
identical daughter nuclei.
The nucleus of a eukaryotic cell can divide to form two genetically
identical nuclei by a process called mitosis. Mitosis allows the cell to
divide into two daughter cells, each with one of the nuclei and therefore
genetically identical to the other.
B efore mitosis can occur, all of the D NA in the nucleus must be
replicated. This happens during interphase, the period before mitosis.
E ach chromosome is converted from a single D NA molecule into two
identical D NA molecules, called chromatids. D uring mitosis, one of these
chromatids passes to each daughter nucleus.
Mitosis is involved whenever cells with genetically identical nuclei are
required in eukaryotes: during embryonic development, growth, tissue
repair and asexual reproduction.
Although mitosis is a continuous process, cytologists have divided the
events into four phases: prophase, metaphase, anaphase and telophase.  Figure 1 Hydra viridissima with a small
The events that occur in these phases are described in a later section of new polyp attached, produced by asexual
this sub- topic. reproduction involving mitosis

51
1 C E LL B I O LO G Y

Interphase
Activity
There is a limit to how many times Interphase is a very active phase o the cell cycle with
most cells in an organism can undergo many processes occurring in the nucleus and cytoplasm.
mitosis. Cells taken rom a human The cell cycle is the seque nce o events b etween one cell division
embryo will only divide between and the next. It has two main phases: interphase and cell division.
40 and 60 times, but given that Interphase is a very active phase in the lie o a cell when many
the number o cells doubles with metabolic reactions occur. S ome o these, such as the reactions o
each division, it is easily enough to cell respiration, also occur during cell division, b ut D NA replication
produce an adult human body. There in the nucleus and protein synthesis in the cytoplasm only happen
are exceptions where much greater during interphase.
numbers o divisions can occur, such
as the germinal epithelium in the During interphase the numbers o mitochondria in the cytoplasm increase.
testes. This is a layer o cells that This is due to the growth and division o mitochondria. In plant cells and
divides to provide cells used in sperm algae the numbers o chloroplasts increase in the same way. They also
production. Discuss how many times synthesize cellulose and use vesicles to add it to their cell walls.
the cells in this layer might need to Interphase consists o three phases, the G 1 phase, S phase and G 2 phase.
divide during a man's lie. In the S phase the cell replicates all the genetic material in its nucleus, so
that ater mitosis both the new cells have a complete set o genes. Some
do not progress beyond G 1 , because they are never going to divide so do
not need to prepare or mitosis. They enter a phase called G 0 which may
be temporary or permanent.

G2 Supercoiling of chromosomes
Mitosis
s Chromosomes condense by supercoiling during mitosis.
in esi
Cy t o k During mitosis, the two chromatids that make up each chromosome must
I N TE

S PH A be separated and moved to opposite poles o the cell. The DNA molecules
R

Each of the
chromosomes
SE
1 G in these chromosomes are immensely long. Human nuclei are on average
is duplicated Cellular contents,
apart from the less than 5 m in diameter but D NA molecules in them are more than
chromosomes
are duplicated. 5 0,000 m long. It is thereore essential to package chromosomes into
much shorter structures. This process is known as condensation o
chromosomes and it occurs during the frst stage o mitosis.
G0
Condensation occurs by means repeatedly coiling the DNA molecule to
make the chromosome shorter and wider. This process is called supercoiling.
Proteins called histones that are associated with DNA in eukaryote
 Figure 2 The cell cycle chromosomes help with supercoiling and enzymes are also involved.

Phases of mitosis
Identifcation o phases o mitosis in cells viewed with a microscope.
There are large numbers o dividing cells in the To be able to identiy the our stages o mitosis,
tips o growing roots. I root tips are treated it is necessary to understand what is happening
chemically to allow the cells to be separated, they in them. Ater studying the inormation in this
can be squashed to orm a single layer o cells on a section you should be able to observe dividing
microscope slide. S tains that bind to D NA are used cells using a microscope or in a micrograph and
to make the chromosomes visible and stages o assign them to one o the phases.
mitosis can then be observed using a microscope.

52
1 . 6 ce ll d I VI s I o n

Prophase
The chromosomes become
shorter and atter by coiling. To
become short enough they have
to coil repeatedly. This is called
supercoiling. The nucleolus breaks
down. Microtubules grow rom
structures called microtubule
organizing centres (MTOC) to orm
 Interphase  chromosomes are  Prophase  nucleoli visible
a spindle-shaped array that links
visible inside the nuclear membrane in the nucleus but no
the poles o the cell. At the end o
prophase the nuclear membrane centromere MTOC individual chromosomes
breaks down.
microtubules

nuclear envelope
disintegrates
chromosome
consisting of two spindle
sister chromatids microtubules
 Early prophase  Late prophase

Metaphase
Microtubules continue to grow
and attach to the centromeres Metaphase
on each chromosome. The two plate equator
attachment points on opposite
sides o each centromere allow the
chromatids o a chromosome to
mitotic spindle
attach to microtubules rom diferent
poles. The microtubules are all put
under tension to test whether the
 Metaphase  chromosomes  Metaphase
attachment is correct. This happens aligned on the equator and not
by shortening o the microtubules at inside a nuclear membrane
the centromere. I the attachment is
correct, the chromosomes remain on
the equator o the cell.
Anaphase
At the start o anaphase, each
centromere divides, allowing
the pairs o sister chromatids to
separate. The spindle microtubules
pull them rapidly towards the
poles o the cell. Mitosis produces
two genetically identical nuclei Daughter
because sister chromatids are chromosomes
pulled to opposite poles. This separate
is ensured by the way that the
 Anaphase  two groups of V-shaped  Anaphase
spindle microtubules were
chromatids pointing to the two poles
attached in metaphase.

53
1 C E LL B I O LO G Y

Telophase
The chromatids have reached
the poles and are now called
chromosomes. At each pole the
chromosomes are pulled into a
tight group near the MTOC and
a nuclear membrane reforms
around them. The chromosomes
uncoil and a nucleolus is formed.  Telophase  tight groups of  Interphase  nucleoli visible
By this stage of mitosis the cell is chromosomes at each pole, new inside the nuclear membranes
usually already dividing and the cell wall forming at the equator but not individual chromosomes
two daughter cells enter interphase
again.

Cleavage furrow

Nuclear envelope
forming

 Telophase

data-base questions: Centromeres and telomeres


Figure 3 and the other micrographs on the preceeding pages show
cells undergoing mitosis. In gure 3 , D NA has been stained blue. The
centromeres have been stained with a red fuorescent dye. At the
ends o the chromosomes there are structures called telomeres. These
have been stained with a green fuorescent dye.
1 D educe the stage o mitosis that the cell was in, giving reasons
or your answer. [3 ]
2 The cell has an even number o chromosomes.
a) S tate how many chromosomes there are in this cell. [1 ]
b) E xplain the reason or body cells in plants and animals
having an even number o chromosomes. [2 ]
c) In the micrograph o a cell in interphase, the centromeres
 Figure 3 Cell in mitosis
are on one side o the nucleus and the telomeres are on
the other side. S uggest reasons or this. [2 ]
d) An enzyme called telomerase lengthens the telomeres, by
adding many short repeating base sequences o DNA. This
enzyme is only active in the germ cells that are used to
produce gametes. When DNA is replicated during the cell
cycle in body cells, the end o the telomere cannot be replicated,
so the telomere becomes shorter. Predict the consequences or
a plant or animal o the shortening o telomeres. [2 ]

54
1 . 6 ce ll d I VI s I o n

The mitotic index


Determination o a mitotic index rom a micrograph.
The mitotic index is the ratio between the number o cells in mitosis
in a tissue and the total number o observed cells. It can be calculated
using this equation:
number o cells in mitosis
Mitotic index = ___
total number o cells
Figure 4 is a micrograph o cells rom a tumour that has developed
rom a Leydig cell in the testis. The mitotic index or this tumour can
be calculated i the total number o cells in the micrograph is counted
and also the number o cells in meiosis.
To fnd the mitotic index o the part o a root tip where cells are
prolierating rapidly, these instructions can be used:
 Obtain a prepared slide o an onion or garlic root tip. Find
and examine the meristematic region, i.e. a region o rapid cell division.
Figure 4 Cells undergoing mitosis in a Leydig
 C reate a tally chart. C lassiy each o about a hundred cells in this cell tumour
region as being either in interphase or in any o the stages o mitosis.
 Use this data to calculate the mitotic index.

Cytokinesis
Cytokinesis occurs ater mitosis and is diferent in plant
and animal cells.
C ells can divide ater mitosis when two genetically identical nuclei are
present in a cell. The process o cell division is called cytokinesis. It
usually begins beore mitosis has actually been completed and it happens
in a dierent way in plant and animal cells.
In animal cells the plasma membrane is pulled inwards around the
equator o the cell to orm a cleavage urrow. This is accomplished using
a ring o contractile protein immediately inside the plasma membrane
at the equator. The proteins are actin and myosin and are similar to
proteins that cause contraction in muscle. When the cleavage urrow
reaches the centre, the cell is pinched apart into two daughter cells.
In plant cells vesicles are moved to the equator where they use to orm
tubular structures across the equator. With the usion o more vesicles
these tubular structures merge to orm two layers o membrane across the
whole o the equator, which develop into the plasma membranes o the
two daughter cells and are connected to the existing plasma membranes at
the sides o the cell, completing the division o the cytoplasm.
The next stage in plants is or pectins and other substances to be
brought in vesicles and deposited by exocytosis between the two new
membranes. This orms the middle lamella that will link the new cell
walls. B oth o the daughter cells then bring cellulose to the equator and
deposit it by exocytosis adj acent to the middle lamella. As a result, each  Figure 5 Cytokinesis in (a) fertilized sea urchin
cell builds its own cell wall adj acent to the equator. egg (b) cell from shoot tip of Coleus plant

55
1 C E LL B I O LO G Y

Cyclins and the control of the cell cycle


Cyclins are involved in the control o the cell cycle.
Each o the phases o the cell cycle involves many important tasks. A
group o proteins called cyclins is used to ensure that tasks are perormed
at the correct time and that the cell only moves on to the next stage o
the cycle when it is appropriate.
C yclins bind to enzymes called cyclin- dependent kinases. These kinases
then become active and attach phosphate groups to other proteins in the
cell. The attachment o phosphate triggers the other proteins to become
active and carry out tasks specifc to one o the phases o the cell cycle.
There are our main types o cyclin in human cells. The graph in fgure 6
shows how the levels o these cyclins rise and all. Unless these cyclins reach
a threshold concentration, the cell does not progress to the next stage o the
cell cycle. Cyclins thereore control the cell cycle and ensure that cells divide
when new cells are needed, but not at other times.
concentration

G 1 phase S phase G 2 phase mitosis

Cyclin D triggers cells to move from G 0 to G 1 and from G 1 into S phase.


Cyclin E prepares the cell for DNA replication in S phase.
Cyclin A activates DNA replication inside the nucleus in S phase.
Cyclin B promotes the assembly of the mitotic spindle and other tasks
in the cytoplasm to prepare for mitosis.
 Figure 6

Discovery of cyclins
Serendipity and scientifc discoveries: the discovery o cyclins was accidental.
During research into the control o protein synthesis Further research revealed other cyclins and
in sea urchin eggs, Tim Hunt discovered a protein confrmed what Hunt had suspected rom an early
that increased in concentration ater ertilization then stage  that cyclins are a key actor in the control
decreased in concentration, unlike other proteins o the cell cycle. Tim Hunt was awarded a Nobel
which continued to increase. The protein was being Prize or Physiology in 2 001 to honour his work
synthesized over a period o about 30 minutes and in the discovery o cyclins. His Nobel Lecture can
then soon ater was being broken down. Further be downloaded rom the internet and viewed.
experiments showed that the protein went through In it he mentions the importance o serendipity
repeated increases and decreases in concentration several times because he had not set out to
that coincided with the phases o the cell cycle. The discover how the cell cycle is controlled. This
breakdown occurred about ten minutes ater the discovery is an example o serendipity  a happy
start o mitosis. Hunt named the protein cyclin. and unexpected discovery made by accident.

56
1 . 6 ce ll d I VI s I o n

tumur frmai a ar


Aiviy
Mutagens, oncogenes and metastasis are involved in the car rarh
development o primary and secondary tumours. Tumours can orm in any tissue at any
Tumours are abnormal groups o cells that develop at any stage o lie in age, but the skin, lung, large intestine
any part o the body. In some cases the cells adhere to each other and (bowel) , breast and prostate gland are
do not invade nearby tissues or move to other parts o the body. These particularly vulnerable. Cancer is a
tumours are unlikely to cause much harm and are classifed as benign. major cause o death in most human
In other tumours the cells can become detached and move elsewhere populations so there is a pressing
in the body and develop into secondary tumours. These tumours are need to fnd methods o prevention
malignant and are very likely to be lie- threatening. and treatment. This involves basic
D iseases due to malignant tumours are commonly known as cancer
research into the control o the cell
and have diverse causes. C hemicals and agents that cause cancer are
cycle. Great progress has been made
known as carcinogens, because carcinomas are malignant tumours.
but more is needed.
There are various types o carcinogens including some viruses. All Who should pay or research into
mutagens are carcinogenic, both chemical mutagens and also high cancer?
energy radiation such as X- rays and short- wave ultraviolet light. This is
because mutagens are agents that cause gene mutations and mutations
can cause cancer.
Mutations are random changes to the base sequence o genes. Most
genes do not cause cancer i they mutate. The ew genes that can
become cancer-causing ater mutating are known as oncogenes. In a
normal cell oncogenes are involved in the control o the cell cycle and
cell division. This is why mutations in them can result in uncontrolled
cell division and thereore tumour ormation.
S everal mutations must occur in the same cell or it to become a tumour
cell. The chance o this happening is extremely small, but because
there are vast numbers o cells in the body, the total chance o tumour
ormation during a lietime is signifcant. When a tumour cell has been
ormed it divides repeatedly to orm two, then our, then eight cells and
so on. This group o cells is called a primary tumour. Metastasis is the
movement o cells rom a primary tumour to set up secondary tumours
in other parts o the body.

Smoking and cancer


The correlation between smoking and incidence o
cancers.
A correlation in science is a relationship between two variable
actors. The relationship between smoking and cancer is an example
o a correlation. There are two types o correlation. With a positive
correlation, when one actor increases the other one also increases;
they also decrease together. With a negative correlation, when one
actor increases the other decreases.
There is a positive correlation between cigarette smoking and the
death rate due to cancer. This has been shown repeatedly in surveys.
table 1 shows the results o one o the largest surveys, and the longest

57
1 C E LL B I O LO G Y

continuous one. The data shows that the more cigarettes smoked per
day, the higher the death rate due to cancer. They also show a higher
death rate among those who smoked at one time but had stopped.
The results o the survey also show huge increases in the death
rate due to cancers o the mouth, pharynx, larynx and lung. This
is expected as smoke rom cigarettes comes into contact with each
o these parts o the body, but there is also a positive correlation
between smoking and cancers o the esophagus, stomach, kidney,
bladder, pancreas and cervix. Although the death rate due to other
cancers is not signifcantly dierent in smokers and non- smokers,
table 1 shows smokers are several times more likely to die rom all
cancers than non- smokers.

It is important in science to distinguish between a correlation and a


cause. Finding that there is a positive correlation between smoking
and cancer does not prove that smoking causes cancer. However,
in this case the causal links are well established. C igarette smoke
contains many dierent chemical substances. Twenty o these
have been shown in experiments to cause tumours in the lungs o
laboratory animals or humans. There is evidence that at least orty
other chemicals in cigarette smoke are carcinogenic. This leaves little
doubt that smoking is a cause o cancer.

caue o death etween 1951 Mortaity rate per 100,000 men/year


and 2001 lieong former current moker (igarette/day)
(sampe ize: 34,439 mae non-moker igarette
dotor in britain) moker 114 1524 25

All cancers 360 466 588 747 1,061


Lung cancer 17 68 131 233 417
Cancer of mouth, pharynx,
9 26 36 47 106
larynx and esophagus
All other cancers 334 372 421 467 538
 Table 1 from British Medical Journal 328(7455) June 24 2004

58
1 . 6 ce ll d I VI s I o n

daa-ba qui: The efect o smoking on health


One o the largest ever studies o the eect o death was recorded or each o the doctors who died
smoking on health involved 34,439 male British during this period. The table below shows some
doctors. Inormation was collected on how much o the results. The fgures given are the number o
they smoked rom 1 951 to 2001 and the cause o deaths per hundred thousand men per year.

114 1524
>25 igar
typ f ia n-mkr igar igar
pr ay
pr ay pr ay
Respiratory (diseases o the lungs
107 237 310 471
and airways)
Circulatory (diseases o the heart and
1,037 1,447 1,671 1,938
blood vessels)
Stomach and duodenal ulcers 8 11 33 34
Cirrhosis o the liver 6 13 22 68
Parkinsons disease 20 22 6 18

1 D educe whether there is a positive correlation 4 D iscuss whether the data p roves that
between smoking and the mortality rate smoking is a cause o cirrhosis o the
due to all types o disease. [2 ] liver. [3 ]
2 Using the data in the table, discuss whether the 5 The table does not include deaths due to
threat to health rom smoking is greater with cancer. The survey showed that seven types
respiratory or with circulatory diseases. [4] o cancer are linked with smoking. Suggest
3 Discuss whether the data suggests that smoking three cancers that you would expect
a small number o cigarettes is sae. [3] smoking to cause. [3 ]

59
1 C E LL B I O LO G Y

Questions
1 Figure 7 represents a cell rom a multicellular c) E xplain the dierence in area o the inner
organism. and outer mitochondrial membranes. [3 ]
d) Using the data in the table, identiy two o
the main activities o liver cells. [2 ]

3 In human secretory cells, or example in the lung


and the pancreas, positively charged ions are
pumped out, and chloride ions ollow passively
through chloride channels. Water also moves rom
the cells into the liquid that has been secreted.
In the genetic disease cystic brosis, the chloride
 Figure 7 channels malunction and too ew ions move
out o the cells. The liquid secreted by the cells
a) Identiy, with a reason, whether the cell is becomes thick and viscous, with associated
( i) prokaryotic or eukaryotic; [1 ] health problems.
( ii) part o a root tip or a nger tip; [1 ] a) S tate the names o the processes that:
( iii) in a phase o mitosis or in interphase. [1 ] ( i) move positively charged ions out o
b) The magnication o the drawing is 2 ,5 00  . the secretory cells [1 ]
( i) C alculate the actual size o the cell. [2 ] ( ii) move chloride ions out o the
secretory cells. [1 ]
( ii) C alculate how long a 5 m scale
bar should be i it was added to the ( iii) move water out o the secretory cells. [1 ]
drawing. [1 ] b) Explain why the fuid secreted by people
c) Predict what would happen to the cell i it was with cystic brosis is thick and viscous. [4]
placed in a concentrated salt solution or one
hour. Include reasons or your answer. [3]
4 The amount o D NA present in each cell
nucleus was measured in a large number
2 Table 2 shows the area o membranes in a rat o cells taken rom two dierent cultures o
liver cell. human bone marrow ( gure 8) .
a) For each label ( I, II and III) in the S ample B
Membrane component Area (m 2 ) graph, deduce which phase o the cell cycle
Plasma membrane 1,780 the cells could be in; i.e. G1 , G2 or S . [3 ]
b) Estimate the approximate amount o D NA
Rough endoplasmic reticulum 30,400
per nucleus that would be expected in the
Mitochondrial outer membrane 7,470 ollowing human cell types:

Mitochondrial inner membrane 39,600 ( i) bone marrow at prophase


( ii) bone marrow at telophase. [2 ]
Nucleus 280
Sample A Sample B
Lysosomes 100
Number of cells (in thousands)
Number of cells (in thousands)

3 (non-dividing cell culture) 3 (rapidly dividing cell culture)


Other components 18,500 I
2 2
 Table 2 III
1 1
a) C alculate the total area o membranes in the
liver cell. [2 ] II
b) C alculate the area o plasma membrane as 5 10 15 5 10 15
a percentage o the total area o membranes DNA/pg per nucleus DNA/pg per nucleus
in the cell. S how your working. [3 ]  Figure 8
60
2 M o le cu lar B I o lo GY
Intdtin
Water is the medium for life. Living organisms hydrogen and oxygen are used to supply and
control their composition by a complex web store energy. Many proteins act as enzymes to
of chemical reactions that occur within this control the metabolism of the cell and others
medium. Photosynthesis uses the energy in have a diverse range of biological functions.
sunlight to supply the chemical energy needed Genetic information is stored in D NA and can
for life and cell respiration releases this energy be accurately copied and translated to make the
when it is needed. C ompounds of carbon, proteins needed by the cell.

2.1 Molecules to metabolism


undstnding appitins
 Molecular biology explains living processes in
 Urea as an example o a compound that is
terms o the chemical substances involved. produced by living organisms but can also be
 Carbon atoms can orm our bonds allowing a artifcially synthesized.
diversity o compounds to exist.
 Lie is based on carbon compounds
including carbohydrates, lipids, proteins and Skis
nucleic acids.  Drawing molecular diagrams o glucose, ribose, a
 Metabolism is the web o all the enzyme saturated atty acid and a generalized amino acid.
catalysed reactions in a cell or organism.  Identifcation o biochemicals such as
 Anabolism is the synthesis o complex carbohydrate, lipid or protein rom
molecules rom simpler molecules including molecular diagrams.
the ormation o macromolecules rom
monomers by condensation reactions.
 Catabolism is the breakdown o complex
Nt f sin
molecules into simpler molecules including the  Falsifcation o theories: the artifcial synthesis
hydrolysis o macromolecules into monomers. o urea helped to alsiy vitalism.

61
2 M O L E C U L AR B I O LO G Y

Molecular biology
Molecular biology explains living processes in terms
o the chemical substances involved.
The discovery o the structure o D NA in 1 95 3 started a revolution in
biology that has transormed our understanding o living organisms. It
raised the possibility o explaining biological processes rom the structure
o molecules and how they interact with each other. The structures are
diverse and the interactions are very complex, so although molecular
 Figure 1 A molecular biologist at work in the biology is more than 5 0 years old, it is still a relatively young science.
laboratory Many molecules are important in living organisms including one as
apparently simple as water, but the most varied and complex molecules
are nucleic acids and proteins. Nucleic acids comprise D NA and RNA.
They are the chemicals used to make genes. Proteins are astonishingly
varied in structure and carry out a huge range o tasks within the
cell, including controlling chemical reactions o the cell by acting as
enzymes. The relationship between genes and proteins is at the heart
o molecular biology.
The approach o the molecular biologist is reductionist as it involves
considering the various biochemical processes o a living organism
and breaking down into its component parts. This approach has been
immensely productive in biology and has given us insights into whole
organisms that we would not otherwise have. Some biologists argue
that the reductionist approach o the molecular biologist cannot explain
everything though, and that when component parts are combined there
are emergent properties that cannot be studied without looking at the
whole system together.

Synthesis of urea
Urea as an example o a compound that is produced by
living organisms but can also be artifcially synthesized.
Urea is a nitrogen- containing compound with a relatively simple
molecular structure ( fgure 2 ) . It is a component o urine and this was
where it was frst discovered. It is produced when there is an excess
o amino acids in the body, as a means o excreting the nitrogen
rom the amino acids. A cycle o reactions, catalysed by enzymes, is
used to produce it ( fgure 3 ) . This happens in the liver. Urea is then
transported by the blood stream to the kidneys where it is fltered out
and passes out o the body in the urine.
Urea can also be synthesized artifcially. The chemical reactions used
are dierent rom those in the liver and enzymes are not involved, but
O the urea that is produced is identical.
ammonia + carbon dioxide  ammonium carbamate
C
 urea + water
H 2N NH 2
About 1 00 million tonnes are produced annually. Most o this is used
 Figure 2 Molecular diagram of urea as a nitrogen ertilizer on crops.

62
2 .1 M o le c u le s to M e tab o li s M

CO 2 + NH 3
enzyme 1

carbamoyl phosphate

ornithine

urea
enzyme 2
arginase

citrulline arginine

aspartate
fumarate

enzyme 3 enzyme 4
argininosuccinate

 Figure 3 The cycle of reactions occurring in liver cells that is used to synthesize urea

urea and the alsifcation o vitalism


Falsifcation o theories: the artifcial synthesis o urea helped to alsiy vitalism.
Urea was discovered in urine in the 1 720s and was organic compounds could be as well. Whlers
assumed to be a product o the kidneys. At that achievement was evidence against the theory
time it was widely believed that organic compounds o vitalism. It helped to alsiy the theory, but it
in plants and animals could only be made with the did not cause all biologists to abandon vitalism
help o a vital principle. This was part o vitalism  immediately. It usually requires several pieces o
the theory that the origin and phenomena o lie evidence against a theory or most biologists to
are due to a vital principle, which is dierent rom accept that it has been alsifed and sometimes
purely chemical or physical orces. Aristotle used controversies over a theory continue or decades.
the word psyche or the vital principle  a Greek
Although biologists now accept that processes
word meaning breath, lie or soul.
in living organisms are governed by the same
In 1 82 8 the German chemist Friedrich Whler chemical and physical orces as in non- living
synthesized urea artifcially using silver matter, there remain some organic compounds
isocyanate and ammonium chloride. This was that have not been synthesized artifcially. It is
the frst organic compound to be synthesized still impossible to make complex proteins such
artifcially. It was a very signifcant step, because as hemoglobin, or example, without using
no vital principle had been involved in the ribosomes and other components o cells. Four
synthesis. Whler wrote this excitedly to the years ater his synthesis o urea, Whler wrote
S wedish chemist Jns Jacob B erzelius: this to B erzelius:
In a manner of speaking, I can no longer Organic chemistry nowadays almost
hold my chemical water. I must tell you drives one mad. To me it appears like a
that I can make urea without the kidneys primeval tropical forest full of the most
of any animal, be it man or dog. remarkable things; a dreadful endless
jungle into which one dare not enter, for
An obvious deduction was that i urea had been
there seems no way out.
synthesized without a vital principle, other

63
2 M O L E C U L AR B I O LO G Y

carbon ompounds
ativity
crbon ompounds Carbon atoms can orm our bonds allowing a diversity
Can you fnd an example o compounds to exist.
o a biological molecule C arbon is only the 1 5 th most abundant element on Earth, but it can be
in which a carbon atom is used to make a huge range of different molecules. This has given living
bonded to atoms o three organisms almost limitless possibilities for the chemical composition and
other elements or even our activities of their cells. The diversity of carbon compounds is explained
other elements? by the properties of carbon.
Titin is a giant protein that Carbon atoms form covalent bonds with other atoms. A covalent bond
acts as a molecular spring is formed when two adjacent atoms share a pair of electrons, with one
in muscle. The backbone o electron contributed by each atom. Covalent bonds are the strongest type of
the titin molecule is a chain bond between atoms so stable molecules based on carbon can be produced.
o 100,000 atoms, linked by
Each carbon atom can form up to four covalent bonds  more than
single covalent bonds.
most other atoms, so molecules containing carbon can have complex
Can you fnd an example structures. The bonds can be with other carbon atoms to make rings
o a molecule in your or chains of any length. Fatty acids contain chains of up to 2 0 carbon
body with a chain o over atoms for example. The bonds can also be with other elements such as
1,000,000,000 atoms? hydrogen, oxygen, nitrogen or phosphorus.
C arbon atoms can bond with just one other element, such as hydrogen in
methane, or they can bond to more than one other element as in ethanol
( alcohol found in beer and wine) . The four bonds can all be single
covalent bonds or there can be two single and one double covalent bond,
H for example in the carboxyl group of ethanoic acid (the acid in vinegar) .
H C H methane

H classifying arbon ompounds


H H
Lie is based on carbon compounds including
H C C O H ethanol carbohydrates, lipids, proteins and nucleic acids.
H H Living organisms use four main classes of carbon compound. They have
different properties and so can be used for different purposes.
H
O
Carbohydrates are characterized by their composition. They are composed
H C C ethanoic acid
of carbon, hydrogen and oxygen, with hydrogen and oxygen in the ratio of
O H
H two hydrogen atoms to one oxygen, hence the name carbohydrate.
Lip ids are a broad class of
H H H H H H H H H H H H H H H H H molecules that are insoluble in
O
water, including steroids, waxes,
H C C C C C C C C C C C C C C C C C C
OH
fatty acids and triglycerides. In
H H H H H H H H H H H common language, triglycerides
linolenic acid  an omega-3 fatty acid are fats if they are solid at room
 Figure 4 Some common naturally-occurring carbon compounds temperature or oils if they are
liquid at room temperature.
Proteins are composed of one or more chains of amino acids. All of the
amino acids in these chains contain the elements carbon, hydrogen, oxygen
and nitrogen, but two of the twenty amino acids also contain sulphur.
Nucleic acids are chains of subunits called nucleotides, which contain
carbon, hydrogen, oxygen, nitrogen and phosphorus. There are two types
of nucleic acid: ribonucleic acid ( RNA) and deoxyribonucleic acid ( D NA) .

64
2 .1 M o le c u le s to M e tab o li s M

Drawing molecules
Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a
generalized amino acid.
There is no need to memorize the structure o atom is represented with C and an oxygen atom
many dierent molecules but a biologist should with O . S ingle covalent bonds are shown with a
be able to draw diagrams o a ew o the most line and double bonds with two lines.
important molecules.
S ome chemical groups are shown with the
Each atom in a molecule is represented using the atoms together and bonds not indicated. Table 1
symbol o the element. For example a carbon gives examples.

Name of group Full structure Simplied notation

hydroxyl O H OH
H
amine N NH 2
H
O
carboxyl C COOH
O H

methyl C H CH 3

 Table 1

Ribose OH
 The ormula or ribose is C 5 H 1 0 O 5 5
H C H
 The molecule is a fve- membered ring with a side chain. O OH
4
CH H C1
 Four carbon atoms are in the ring and one orms the side chain. H H
3 C C2
 The carbon atoms can be numbered starting with number 1 on the right.
OH OH
 The hydroxyl groups ( O H) on carbon atoms 1 , 2 and 3 point up,
down and down respectively.  Ribose
6 CH 2 OH
Glucose 5
C
C O
 The ormula or glucose is C 6 H 1 2 O 6 H H
4C OH H 1 C
 The molecule is a six- membered ring with a side chain. HO C C OH
3 2
 Five carbon atoms are in the ring and one orms the side chain.
H OH
 The carbon atoms can be numbered starting with number 1 on the right.  Glucose
 The hydroxyl groups ( O H) on carbon atoms 1 , 2 , 3 and 4 point
down, down, up and down respectively, although in a orm o
glucose used by plants to make cellulose the hydroxyl group on
carbon atom 1 points upwards.

65
2 M O L E C U L AR B I O LO G Y

Saturated fatty acids O OH


C
 The carbon atoms form an unbranched chain.
H C H
 In saturated fatty acids they are bonded to each other by single bonds. H C H
 The number of carbon atoms is most commonly between 1 4 and 2 0. H C H
H C H
 At one end of the chain the carbon atom is part of a carboxyl group
H C H
 At the other end the carbon atom is bonded to three hydrogen atoms.
H C H
 All other carbon atoms are bonded to two hydrogen atoms. H C H
H C H
Amino acids H C H
 A carbon atom in the centre of the molecule is bonded to four H C H
different things: H C H
 an amine group, hence the term amino acid; H C H
 a carboxyl group which makes the molecule an acid; H C H
H C H
 a hydrogen atom;
H C H
 the R group, which is the variable part of amino acids.
H
O
R R  Full molecular diagram o a
H O saturated atty acid
N C C CH 3 (CH 2 ) n C
N 2N C COOH
H O H
H H OH
full molecular diagram simplied molecular diagram  Simplifed molecular diagram
 Molecular diagrams o an amino acid o a saturated atty acid

Identifying molecules
Identifcation o biochemicals as carbohydrate, lipid or protein rom molecular
diagrams.
The molecules of carbohydrates, lipids and
proteins are so different from each other that it is
usually quite easy to recognize them.
 Proteins contain C , H, O and N whereas
carbohydrates and lipids contain C , H and O
but not N.
 Many proteins contain sulphur ( S ) but
carbohydrates and lipids do not.
 C arbohydrates contain hydrogen and oxygen
atoms in a ratio of 2 :1 , for example glucose
is C 6 H 1 2 O 6 and sucrose ( the sugar commonly
used in baking) is C 1 2 H 22 O 1 1
 Lipids contain relatively less oxygen than
carbohydrates, for example oleic acid ( an
unsaturated fatty acid) is C 1 8 H 34O 2 and the
steroid testosterone is C 1 9 H 28 O 2  Figure 5 A commonly-occurring biological molecule

66
2 .1 M o le c u le s to M e tab o li s M

Metbolism
Metabolism is the web of all the enzyme catalysed
reactions in a cell or organism.
All living organisms carry out large numbers o dierent chemical
reactions. These reactions are catalysed by enzymes. Most o them
happen in the cytoplasm o cells but some are extracellular, such as the
reactions used to digest ood in the small intestine. Metabolism is the
sum o all reactions that occur in an organism.
Metabolism consists o pathways by which one type o molecule is transormed
into another, in a series o small steps. These pathways are mostly chains o
reactions but there are also some cycles. An example is shown in fgure 3.
E ven in relatively simple prokaryote cells, metabolism consists o over
1 , 000 dierent reactions. Global maps showing all reactions are very
complex. They are available on the internet, or example in the Kyoto
E ncyclopedia o Genes and Genomes.

anbolism
Anabolism is the synthesis of complex molecules from
simpler molecules including the formation of macromolecules
from monomers by condensation reactions.
Metabolism is oten divided into two parts, anabolism and catabolism.
Anabolism is reactions that build up larger molecules rom smaller ones.
An easy way to remember this is by recalling that anabolic steroids
are hormones that promote body building. Anabolic reactions require
energy, which is usually supplied in the orm o ATP.
Anabolism includes these processes:
 Protein synthesis using ribosomes.
 D NA synthesis during replication.
 Photosynthesis, including production o glucose rom carbon dioxide
and water.
 Synthesis o complex carbohydrates including starch, cellulose and
glycogen.

ctbolism
Catabolism is the breakdown of complex molecules
into simpler molecules including the hydrolysis of
macromolecules into monomers.
C atabolism is the part o metabolism in which larger molecules are
broken down into smaller ones. C atabolic reactions release energy and
in some cases this energy is captured in the orm o ATP, which can then
be used in the cell. C atabolism includes these processes:
 D igestion o ood in the mouth, stomach and small intestine.
 C ell respiration in which glucose or lipids are oxidized to carbon
dioxide and water.
 D igestion o complex carbon compounds in dead organic matter by
decomposers. 67
2 M O L E C U L AR B I O LO G Y

2.2 Water
understnding applictions
 Water molecules are polar and hydrogen bonds
 Comparison of the thermal properties of water
form between them. with those of methane.
 Hydrogen bonding and dipolarity explain  Use of water as a coolant in sweat.
the adhesive, cohesive, thermal and solvent
 Methods of transport of glucose, amino acids,
properties of water.
cholesterol, fats, oxygen and sodium chloride
 Substances can be hydrophilic or hydrophobic. in blood in relation to their solubility in water.

Ntre of science
 Use theories to explain natural phenomena:
the theory that hydrogen bonds form between
water molecules explains waters properties.

H H Hydrogen bonding in wter


Water molecules are polar and hydrogen bonds form
O
between them.
A water molecule is ormed by covalent bonds between an oxygen atom
and two hydrogen atoms. The bond between hydrogen and oxygen
tends to small involves unequal sharing o electrons  it is a polar covalent bond. This
pull the positive
is because the nucleus o the oxygen atom is more attractive to electrons
electrons charge  +
slightly on each than the nuclei o the hydrogen atoms ( fgure 1 ) .
in this hydrogen B ecause o the unequal sharing o electrons in water molecules, the
direction atom
hydrogen atoms have a partial positive charge and oxygen has a partial
Corresponding negative charge
negative charge. B ecause water molecules are bent rather than linear,
2 - on oxygen atom
the two hydrogen atoms are on the same side o the molecule and orm
 Figure 1 Water molecules one pole and the oxygen orms the opposite pole.
Positively charged particles ( positive ions) and negatively charged
particles ( negative ions) attract each other and orm an ionic bond.
Water molecules only have partial charges, so the attraction is less but it
is still enough to have signifcant eects. The attraction between water
molecules is a hydrogen bond. S trictly speaking it is an intermolecular
water molecule orce rather than a bond. A hydrogen bond is the orce that orms when
a hydrogen atom in one polar molecule is attracted to a slightly negative
hydrogen bond
atom o another polar covalent molecule.

 Figure 2 The dotted line Although a hydrogen bond is a weak intermolecular orce, water
indicates the presence of molecules are small, so there are many o them per unit volume o water
an intermolecular force and large numbers o hydrogen bonds ( fgure 2 ) . C ollectively they give
between the molecules. This water its unique properties and these properties are, in turn, o immense
is called a hydrogen bond importance to living things.

68
2 . 2 W at e r

Hydrogen bonds and the properties of water


Use theories to explain natural phenomena: the theory that hydrogen bonds form
between water molecules explains waters properties.
There is strong experimental evidence or hydrogen It might seem unwise to base our understanding
bonds, but it remains a theory that they orm o the natural world on something that has not
between water molecules. Scientists cannot prove been proven to exist. However this is the way
without doubt that they exist as they are not directly that science works  we can assume that a theory
visible. However, hydrogen bonds are a very useul is correct i there is evidence or it, i it helps to
way o explaining the properties o water. They predict behaviour, i it has not been alsifed and
explain the cohesive, adhesive, thermal and solvent i it helps to explain natural phenomena.
properties o water. It is these distinctive properties
that make water so useul to living organisms.

Properties of water
Hydrogen bonding and dipolarity explain the cohesive,
adhesive, thermal and solvent properties of water.
Cohesive properties
C ohesion reers to the binding together o two molecules o the same
type, or instance two water molecules.
Water molecules are cohesive  they cohere, which means they stick to
each other, due to hydrogen bonding, described in the previous section.
This property is useul or water transport in plants. Water is sucked
through xylem vessels at low pressure. The method can only work i
the water molecules are not separated by the suction orces. D ue to
hydrogen bonding this rarely happens and water can be pulled up to the
top o the tallest trees  over a hundred metres.
Adhesive properties
Hydrogen bonds can orm between water and other polar molecules,
causing water to stick to them. This is called adhesion. This property is
useul in leaves, where water adheres to cellulose molecules in cell walls.
I water evaporates rom the cell walls and is lost rom the lea via the
network o air spaces, adhesive orces cause water to be drawn out o
the nearest xylem vessel. This keeps the walls moist so they can absorb
carbon dioxide needed or photosynthesis.
Thermal properties
Water has several thermal properties that are useul to living organisms:
 High specifc heat capacity. Hydrogen bonds restrict the motion o
water molecules and increases in the temperature o water require
hydrogen bonds to be broken. Energy is needed to do this. As a result,
the amount o energy needed to raise the temperature o water is
relatively large. To cool down, water must lose relatively large amounts
o energy. Waters temperature remains relatively stable in comparison
to air or land, so it is a thermally stable habitat or aquatic organisms.
 High latent heat o vap orization. When a molecule evaporates
it separates rom other molecules in a liquid and becomes a vapour
molecule. The heat needed to do this is called the latent heat o
69
2 M O L E C U L AR B I O LO G Y

vaporization. Evaporation therefore has a cooling effect. C onsiderable


amounts of heat are needed to evaporate water, because hydrogen
bonds have to be broken. This makes it a good evaporative coolant.
S weating is an example of the use of water as a coolant.
 High boiling point. The boiling point of a substance is the highest
temperature that it can reach in a liquid state. For the same reasons that
water has a high latent heat of vaporization, its boiling point is high.
Water is therefore liquid over a broad range of temperatures  from 0 C
to 1 00 C. This is the temperature range found in most habitats on Earth.
Solvent properties
Water has important solvent properties. The polar nature of the water
molecule means that it forms shells around charged and polar molecules,
preventing them from clumping together and keeping them in solution.
Water forms hydrogen bonds with polar molecules. Its partially negative
oxygen pole is attracted to positively charged ions and its partially
positive hydrogen pole is attracted to negatively charged ions, so both
dissolve. C ytoplasm is a complex mixture of dissolved substances in
which the chemical reactions of metabolism occurs.

toK
Hydrophilic and hydrophobic
How do scientic explanations difer Substances can be hydrophilic or hydrophobic.
rom pseudo-scientic explanations?
The literal meaning of the word hydrophilic is water-loving. It is used to
Homeopathy is a practice where describe substances that are chemically attracted to water. All substances
remedies are prepared by dissolving that dissolve in water are hydrophilic, including polar molecules such
things like charcoal, spider venom as glucose, and particles with positive or negative charges such as
or deadly nightshade. This mother sodium and chloride ions. S ubstances that water adheres to, cellulose for
tincture o harmul substance is diluted example, are also hydrophilic.
again and again to the point where a
sample rom the solution is unlikely to S ome substances are insoluble in water although they dissolve in other
contain a single molecule o the solute. solvents such as propanone ( acetone) . The term hydrophobic is used to
It is this ultra-dilute solution that is describe them, though they are not actually water-fearing. Molecules
claimed to have medicinal properties. are hydrophobic if they do not have negative or positive charges and are
The properties are reerred to as the nonpolar. All lipids are hydrophobic, including fats and oils
memory o water. Despite the large
number o practitioners o this practice,
no homeopathic remedy has ever been
shown to work in a large randomized
placebo-controlled clinical trial.

 Figure 3 When two nonpolar molecules in water come into contact, weak interactions form
between them and more hydrogen bonds form between water molecules
70
2 . 2 W at e r

I a nonpolar molecule is surrounded by water molecules, hydrogen bonds


orm between the water molecules, but not between the nonpolar molecule
and the water molecules. I two nonpolar molecules are surrounded by
water molecules and random movements bring them together, they behave
as though they are attracted to each other. There is a slight attraction
between nonpolar molecules, but more signifcantly, i they are in contact
with each other, more hydrogen bonds can orm between water molecules.
This is not because they are water-earing: it is simply because water
molecules are more attracted to each other than to the nonpolar molecules.
As a result, nonpolar molecules tend to join together in water to orm larger
and larger groups. The orces that cause nonpolar molecules to join together
into groups in water are known as hydrophobic interactions.

comparing water and methane


Comparison o the thermal properties o water with
those o methane.
The properties o water have already been described. Methane is a
waste product o anaerobic respiration in certain prokaryotes that live
in habitats where oxygen is lacking. Methanogenic prokaryotes live
in swamps and other wetlands and in the guts o animals, including
termites, cattle and sheep. They also live in waste dumps and are
deliberately encouraged to produce methane in anaerobic digesters.
Methane can be used as a uel but i allowed to escape into the
atmosphere it contributes to the greenhouse eect.
Water and methane are both small molecules with atoms linked by
single covalent bonds. However water molecules are polar and can
orm hydrogen bonds, whereas methane molecules are nonpolar and
do not orm hydrogen bonds. As a result their physical properties are
very dierent.
The data in table 1 shows some o the physical properties o methane
and water. The density and specifc heat capacity are given or
methane and water in a liquid state. The data shows that water has
a higher specifc heat capacity, higher latent heat o vaporization,
higher melting point and higher boiling point. Whereas methane is
liquid over a range o only 2 2 C , water is liquid over 1 00 C .

Popy Mhn W


Formula CH 4 H 2O
Molecular mass 16 18
3
Density 0.46g per cm 1g per cm 3
Specifc heat capacity 2.2 J per g per C 4.2 J per g per C
Latent heat o vaporization 760 J/g 2,257 J/g
Melting point 182 C 0 C
Boiling point  Figure 4 Bubbles of methane gas, produced by
160 C 100 C
prokaryotes decomposing organic matter at
 Table 1 Comparing methane and water the bottom of a pond have been trapped in ice
when the pond froze
71
2 M O L E C U L AR B I O LO G Y

cooling the body with sweat


Use of water as a coolant in sweat.
Sweat is secreted by glands in the skin. The sweat There are methods o cooling other than sweating,
is carried along narrow ducts to the surace o the though many o these also rely on heat loss due
skin where it spreads out. The heat needed or the to evaporation o water. Panting in dogs and birds
evaporation o water in sweat is taken rom the is an example. Transpiration is evaporative loss
tissues o the skin, reducing their temperature. o water rom plant leaves; it has a cooling eect
B lood fowing through the skin is thereore which is useul in hot environments.
cooled. This is an eective method o cooling
the body because water has a high latent heat o
vaporization. S olutes in the sweat, especially ions
such as sodium, are let on the skin surace and
can sometimes be detected by their salty taste.
Sweat secretion is controlled by the hypothalamus
o the brain. It has receptors that monitor blood
temperature and also receives sensory inputs rom
temperature receptors in the skin. I the body is
overheated the hypothalamus stimulates the sweat
glands to secrete up to two litres o sweat per hour.
Usually no sweat is secreted i the body is below
the target temperature, though when adrenalin is
secreted we sweat even i we are already cold. This
is because adrenalin is secreted when our brain
anticipates a period o intense activity that will
tend to cause the body to overheat.

Transport in blood plasma


Methods of transport of glucose, amino acids, cholesterol, fats, oxygen and
sodium chloride in blood in relation to their solubility in water.
B lood transports a wide variety o substances, Glucose is a polar molecule. It is reely soluble in
using several methods to avoid possible problems water and is carried dissolved in blood plasma.
and ensure that each substance is carried in large
O xygen is a nonpolar molecule. B ecause o the
enough quantities or the bodys needs.
small size o the molecule it dissolves in water but
S odium chloride is an ionic compound that is only sparingly and water becomes saturated with
reely soluble in water, dissolving to orm sodium oxygen at relatively low concentrations. Also, as
ions ( Na + ) and chloride ions ( C l - ) , which are the temperature o water rises, the solubility o
carried in blood plasma. oxygen decreases, so blood plasma at 3 7 C can
hold much less dissolved oxygen than water at
Amino acids have both negative and positive
2 0 C or lower. The amount o oxygen that blood
charges. B ecause o this they are soluble in water
plasma can transport around the body is ar too
but their solubility varies depending on the R
little to provide or aerobic cell respiration. This
group, some o which are hydrophilic while others
problem is overcome by the use o hemoglobin in
are hydrophobic. All amino acids are soluble
red blood cells. Hemoglobin has binding sites or
enough to be carried dissolved in blood plasma.
oxygen and greatly increases the capacity o the
blood or oxygen transport.

72
2 . 3 c a r b o h y d r at e s a n d l i P i d s

Fats molecules are entirely nonpolar, are larger


than oxygen and are insoluble in water. They are phospholipid
carried in blood inside lipoprotein complexes. protein
These are groups of molecules with a single layer cholesterol
of phospholipid on the outside and fats inside. The
hydrophilic phosphate heads of the phospholipids triglyceride
face outwards and are in contact with water in
the blood plasma. The hydrophobic hydrocarbon
tails face inwards and are in contact with the
fats. There are also proteins in the phospholipid
monolayer, hence the name lipoprotein.
Cholesterol molecules are hydrophobic, apart
from a small hydrophilic region at one end. This
is not enough to make cholesterol dissolve in
water and instead it is transported with fats in
lipoprotein complexes. The cholesterol molecules
are positioned in the phospholipid monolayers, with
the hydrophilic region facing outwards in the region
with the phosphate heads of the phospholipids.  Figure 5 Arrangement of molecules in a lipoprotein complex

2.3 c  p


understnding applictions
 Monosaccharide monomers are linked
 Structure and unction o cellulose and starch
together by condensation reactions to orm in plants and glycogen in humans.
disaccharides and polysaccharide polymers.
 Scientifc evidence or health risks o trans-ats
 Fatty acids can be saturated, monounsaturated
and saturated ats.
or polyunsaturated.
 Lipids are more suitable or long-term energy
 Unsaturated atty acids can be cis or trans
storage in humans than carbohydrates.
isomers.
 Evaluation o evidence and the methods used
 Triglycerides are ormed by condensation rom
to obtain evidence or health claims made
three atty acids and one glycerol. about lipids.

Ntre of science Skills


 Evaluating claims: health claims made about  Use o molecular visualization sotware to
lipids need to be assessed. compare cellulose, starch and glycogen.
 Determination o body mass index by
calculation or use o a nomogram.

73
2 M O L E C U L AR B I O LO G Y

toK carbohydrates
i w cmpeng paradgms gve
Monosaccharide monomers are linked together by
dferen explanans  a phenmenn, condensation reactions to orm disaccharides and
hw can we decde whch s crrec? polysaccharide polymers.
Thomas Kuhn, in his book The Structure o Glucose, ructose and ribose are all examples o monosaccharides. The
Scientifc Revolutions adopted the word structure o glucose and ribose molecules was shown in sub-topic 2 .1 .
paradigm to reer to the rameworks that Monosaccharides can be linked together to make larger molecules.
dominate the interpretation o inormation
in a scientifc discipline at a particular  Monosaccharides are single sugar units.
point in time. The paradigm impacts the  D isaccharides consist o two monosaccharides linked together. For
kinds o questions that are supposed to example, maltose is made by linking two glucose molecules together.
be asked. S ucrose is made by linking a glucose and a ructose.
Nutritionism is the reductionist paradigm  Polysaccharides consist o many monosaccharides linked together.
that the presence o indicator nutrients S tarch, glycogen and cellulose are polysaccharides. They are all made
are the key determinant o healthy by linking together glucose molecules. The dierences between them
ood. Even highly processed ood may are described later in this sub-topic.
be advertised as healthy depending
on the degree to which it contains When monosaccharides combine, they do so by a process called
healthy nutrients. Words like carbs, condensation ( fgure 1 ) . This involves the loss o an O H rom one
vitamins and polyunsaturated at have molecule and an H rom another molecule, which together orm
entered the everyday lexicon. Some H 2 O . Thus, condensation involves the combination o subunits and
argue that this aligns consumer anxiety yields water.
with the commercial interests o ood Linking together monosaccharides to orm disaccharides and
manuacturers. polysaccharides is an anabolic process and energy has to be used to do it.
An alternative paradigm or determining ATP supplies energy to the monosaccharides and this energy is then used
the healthiness o ood is argued or by when the condensation reaction occurs.
Michael Pollan in his book In Deense o
Food. It argues that ood quality should H H H H
Monosaccharides, C 6 H 12 O 6
be determined by cultural tradition which
e.g. glucose, fructose, galactose
tended to look at ood more holistically: HO OH HO OH
The sheer novelty and glamor o
H 2O
the Western diet, with its seventeen
thousand new ood products every year Condensation Hydrolysis
and the marketing power  thirty-two (water removed) (water added)
billion dollars a year  used to sell us
those products, has overwhelmed the H H
Disaccharide, C 12 H 22 O 11
orce otradition and let us where we
e.g. maltose, sucrose, lactose
now fnd ourselves: relying on science HO O OH
and journalism and government and Glycosidic
bond
marketing to help us decide what to eat
Michael Pollan, In Deense oFood: An Condensation Hydrolysis
Eater's Maniesto
H H
Polysaccharide
e.g. starch, glycogen
HO O O O OH
 Figure 1 Condensation and hydrolysis reactions between monosaccharides and
disaccharides

74
2 . 3 c a r b o h y d r at e s a n d l i P i d s

Imaging carbohydrate molecules


Use of molecular visualization software to compare
cellulose, starch and glycogen.
The most widely used molecular visualization software is JMol, which
can be downloaded free of charge. There are also many websites that
use JMol, which are easier to use. S uggestions of suitable websites are
available with the electronic resources that accompany this book.
When JMol software is being used, you should be able to make these
changes to the image of a molecule that you see on the screen:
 Use the scroll function on the mouse to make the image larger
or smaller.
 Left click and move the mouse to rotate the image.
 Right click to display a menu that allows you to change the style
of molecular model, label the atoms, make the molecule rotate
continuously or change the background colour.
S pend some time developing your skill in molecular visualization and
then try these questions to test your skill level and learn more about
the structure of polysaccharides.
Questions
1 Select glucose with the ball and stick style with a black background.
 What colours are used to show carbon, hydrogen and
oxygen atoms? [2 ]
2 S elect sucrose with sticks style and a blue background.
 What is the difference between the glucose ring and the
fructose ring in the sucrose molecule? [1 ]
3 S elect amylose, which is the unbranched form of starch, with
the wireframe style and a white background. If possible select a
short amylose chain and then a longer one.
 What is the overall shape of an amylose molecule? [1 ]
 How many glucose molecules in the chain are linked to
only one other glucose? [1 ]
4 S elect amylopectin, with the styles and colours that you prefer.
Amylopectin is the branched form of starch. Zoom in to look
closely at a position where there is a branch. A glucose molecule
must be linked to an extra third glucose to make the branch.
 What is different about this linkage, compared to the
linkages between glucose molecules in unbranched parts
of the molecule? [1 ]
 How many glucose molecules are linked to only one other  Figure 2 Images of sugars using molecular
glucose in the amylopectin molecule? [1 ] visualization software  (a) fructose,
(b) maltose, (c) lactose

75
2 M O L E C U L AR B I O LO G Y

5 Select glycogen. It is similar but not identical to the


amylopectin orm o starch.
 What is the dierence between glycogen and amylopectin? [1 ]
6 Select cellulose.
 How is it dierent in shape rom the other polysaccharides? [1 ]
7 Look at the oxygen atom that orms part o the ring in each
glucose molecule in the chain.
 What pattern do you notice in the position o these oxygen
atoms along the chain?

Polysaccharides
Structure and function of cellulose and starch in plants and glycogen in humans.
Starch, glycogen and cellulose are all made by linking
together glucose molecules, yet their structure and
unctions are very dierent. This is due to dierences
in the type o glucose used to make them and in the
type o linkage between glucose molecules.
Glucose has fve O H groups, any o which
could be used in condensation reactions, but
only three o them are actually used to link to
make polysaccharides. The most common link is
between the O H on carbon atom 1 ( on the right
hand side in molecular diagrams o glucose) and
the O H on carbon atom 4 ( shown on the let
hand side) . The O H on carbon atom 6 ( shown
at the top o molecular diagrams) is used to orm
side branches in some polysaccharides.  Figure 3 Glucose molecule
Glucose can have the OH group on carbon atom 1
pointing either upwards or downwards. In alpha
glucose (-glucose) the OH group points downwards
but in beta glucose (-glucose) it points upwards.
This small dierence has major consequences or
polysaccharides made rom glucose.
Cellulose is made by linking together -glucose
 Figure 4 Cellulose
molecules. Condensation reactions link carbon atom
1 to carbon atom 4 on the next -glucose. The OH
groups on carbon atom 1 and 4 point in opposite C ellulose molecules are unbranched chains o
directions: up on carbon 1 and down on carbon 4. - glucose, allowing them to orm bundles with
To bring these OH groups together and allow a hydrogen bonds linking the cellulose molecules.
condensation reaction to occur, each -glucose These bundles are called cellulose microfbrils.
added to the chain has to be positioned at 1 80 to They have very high tensile strength and are used
the previous one. The glucose subunits in the chain as the basis o plant cell walls. The tensile strength
are oriented alternately upwards and downwards. o cellulose prevents plant cells rom bursting,
The consequence o this is that the cellulose even when very high pressures have developed
molecule is a straight chain, rather than curved. inside the cell due to entry o water by osmosis.

76
2 . 3 c a r b o h y d r at e s a n d l i P i d s

Starch is made by linking together -glucose


molecules. As in cellulose, the links are made by
condensation reactions between the OH groups on
carbon atom 1 o one glucose and carbon atom 4
o the adjacent glucose. These OH groups both
point downwards, so all the glucose molecules
in starch can be orientated in the same way. The
consequence o this is that the starch molecule is
curved, rather than straight. There are two orms o
starch. In amylose the chain o -glucose molecules
is unbranched and orms a helix. In amylopectin the
chain is branched, so has a more globular shape.
Starch is only made by plant cells. Molecules o both
types o starch are hydrophilic but they are too large
 Figure 5 Starch
to be soluble in water. They are thereore useul
in cells where large amounts o glucose need to be glycogen it is easy to add extra glucose molecules
stored, but a concentrated glucose solution would or remove them. This can be done at both ends
cause too much water to enter a cell by osmosis. o an unbranched molecule or at any o the ends
Starch is used as a store o glucose and thereore o in a branched molecule. S tarch and glycogen
energy in seeds and storage organs such as potato molecules do not have a fxed size and the
cells. Starch is made as a temporary store in lea cells number o glucose molecules that they contain
when glucose is being made aster by photosynthesis can be increased or decreased.
than it can be exported to other parts o the plant.
Glycogen is very similar to the branched orm o
starch, but there is more branching, making the
molecule more compact. Glycogen is made by
animals and also some ungi. It is stored in the
liver and some muscles in humans. Glycogen has
the same unction as starch in plants: it acts as
a store o energy in the orm o glucose, in cells
where large stores o dissolved glucose would
cause osmotic problems. With both starch and

 Figure 6 Glycogen

lipids
Triglycerides are formed by condensation from three fatty
acids and one glycerol.
Lipids are a diverse group o carbon compounds that share the property
o being insoluble in water. Triglycerides are one o the principal groups
o lipid. Examples o triglycerides are the at in adipose tissue in humans
77
2 M O L E C U L AR B I O LO G Y

and the oil in sunfower seeds. Fats are liquid at body temperature
( 3 7 C ) but solid at room temperature ( 2 0 C ) whereas oils are liquid at
both body temperature and room temperature.
A triglyceride is made by combining three atty acids with one glycerol
( see gure 7) . Each o the atty acids is linked to the glycerol by a
condensation reaction, so three water molecules are produced. The
linkage ormed between each atty acid and the glycerol is an ester bond.
This type o bond is ormed when an acid reacts with the O H group in
an alcohol. In this case the reaction is between the C O O H group on a
atty acid and an O H on the glycerol.
Triglycerides are used as energy stores. The energy rom them can be
released by aerobic cell respiration. B ecause they do not conduct heat
well, they are used as heat insulators, or example in the blubber o
Arctic marine mammals.

Glycerol
Fatty acids
H Triglyceride (fat)
H
HO C (CH 2 ) n CH 3 H C O C (CH 2 ) n CH 3
H C O H
O Condensation O
H C O H HO C (CH 2 ) n CH 3 (water removed) H C O C (CH 2 ) n CH 3
O O
H C O H HO C (CH 2 ) n CH 3 H C O C (CH 2 ) n CH 3
H O O
H
3H 2 O
Ester bond
 Figure 7 Formation of a triglyceride from glycerol and three fatty acids

enrgy storag
Lipids are more suitable for long term energy storage in humans than carbohydrates.
Lipids and carbohydrates are both used or energy greater because ats orm pure droplets in
storage in humans, but lipids are normally used cells with no water associated, whereas each
or long- term energy storage. The lipids that are gram o glycogen is associated with about two
used are ats. They are stored in specialized groups grams o water, so lipids are actually six times
o cells called adipose tissue. Adipose tissue is more ecient in the amount o energy that
located immediately beneath the skin and also can be stored per gram o body mass. This
around some organs including the kidneys. is important, because we have to carry our
energy stores around with us wherever we go.
There are several reasons or using lipids
It is even more important or animals such as
rather than carbohydrates or long- term
birds and bats that fy.
energy storage:
 S tored lipids have some secondary roles
 The amount o energy released in cell
that could not be perormed as well by
respiration per gram o lipids is double
carbohydrates. B ecause lipids are poor
the amount released rom a gram o
conductors o heat, they can be used as
carbohydrates. The same amount o energy
heat insulators. This is the reason or much
stored as lipid rather than carbohydrate
o our stored at being in sub- cutaneous
thereore adds hal as much to body mass.
adipose tissue next to the skin. B ecause at
In act the mass advantage o lipids is even

78
2 . 3 c a r b o h y d r at e s a n d l i P i d s

is liquid at body temperature, it can also act can be broken down to glucose rapidly and
as a shock absorber. This is the reason or then transported easily by the blood to where
adipose tissue around the kidneys and some it is needed. Fats in adipose tissue cannot be
other organs. mobilized as rapidly. Glucose can be used either
in anaerobic or aerobic cell respiration whereas
Glycogen is the carbohydrate that is used
ats and atty acids can only be used in aerobic
or energy storage, in the liver and in some
respiration. The liver stores up to 1 5 0 grams
muscles. Although lipids are ideal or long-
o glycogen and some muscles store up to
term storage o energy, glycogen is used or
2 % glycogen by mass.
short- term storage. This is because glycogen

d- qu: Emperor penguins


0.4 0.5
D uring the Antarctic winter emale E mperor
penguins live and eed at sea, but males have 8.0
6.8
to stay on the ice to incubate the single egg the 18.2 14.3
emale has laid. Throughout this time the males
eat no ood. Ater 1 6 weeks the eggs hatch
and the emales return. While the males are 12.0 0.8
incubating the eggs they stand in tightly packed
groups o about 3 , 0 0 0 birds. To investigate the captive before captive after
reasons or standing in groups, 1 0 male birds
were taken rom a colony at Pointe Geologie in 0.4 0.4
Antarctica. They had already survived 4 weeks
6.9
without ood. They were kept or 1 4 more 7.7
17.3 14.4
weeks without ood in enced enclosures
where they could not orm groups. All other
conditions were kept the same as in the wild
11.8
colony. The mean air temperature was 1 6 . 4 C . 2.2
The composition o the captive and the wild
birds bodies was measured beore and ater the wild before wild after
1 4- week period o the experiment. The results
in kilograms are shown in fgure 8 . Key
water
a) C alculate the total mass loss or each lipid
group o birds. [2 ] protein
i) wild other substances
 Figure 8
ii) captive
b) C ompare the changes in lipid content o the
captive birds with those o the birds living
ree in the colony. [2 ]
c) B esides being used as an energy source, state
another unction o lipid which might be
important or penguin survival. [1 ]

79
2 M O L E C U L AR B I O LO G Y

Body mass index


Determination of body mass index by calculation or use
of a nomogram.
The body mass index, usually abbreviated to B MI, was developed
by a B elgian statistician, Adolphe Quetelet. Two measurements are
needed to calculate it: the mass o the person in kilograms and their
height in metres.
B MI is calculated using this ormula:
mass in kilograms
B MI = __2
( height in metres)
Units or B MI are kg m - 2
B MI can also be ound using a type o chart called a nomogram. A
straight line between the height on the let hand scale and the mass
on the right hand scale intersects the B MI on the central scale. The
data based questions on page 81 include a B MI nomogram.
B MI is used to assess whether a persons body mass is at a healthy
level, or is too high or too low. Table 1 shows how this is done:

actvty bMi sttu


etmtng ody ft below 18.5 underweight
prcntg 18.524.9 normal weight
To estimate body fat 25.029.9 overweight
percentage, measure the
thickness of a skinfold in 30.0 or more obese
millimetres using calipers in  Table 1
these four places:
In some parts o the world ood supplies are insufcient or are unevenly
Front of upper arm distributed and many people as a result are underweight. In other parts
Back of upper arm o the world a likelier cause o being underweight is anorexia nervosa.
Below scapula This is a psychological condition that involves voluntary starvation and
Side of waist loss o body mass.
The measurements are
added and then analysis Obesity is an increasing problem
tools available on the internet in some countries. Excessive ood
can be used to calculate intake and insufcient exercise
the estimate. cause an accumulation o at in
adipose tissue. The amount o body
at can be estimated using skinold
calipers (fgure 9) . Obesity increases
the risk o conditions such as
coronary heart disease and type 2
diabetes. It reduces lie expectancy
signifcantly and is increasing
the overall costs o health care in  Measuring body mass. What was this
 Figure 9 Measuring body fat countries where rates o obesity persons body mass index if their height
with skinfold callipers are rising. was 1.80 metres?

80
2 . 3 c a r b o h y d r at e s a n d l i P i d s

d  qu: Nomograms and BMI


Use fgure 1 1 to answer these questions. b) S uggest two ways in which the woman
could reduce her body mass. [2 ]
1 a) S tate the body mass index o a man
who has a mass o 75 kg and a height 4. O utline the relationship between height
o 1 .45  metres. [1 ] and B MI or a fxed body mass. [1 ]
b) Deduce the body mass status o this man. [1 ]
body mass/kg height/cm
2 a) State the body mass o the person standing
on the scales on the previous page. [1 ] 150
125
140
b) The person has a height o 1 .8 metres. 130
D educe their body mass status. [1 ] 130
120 body mass index
3 a) A woman has a height o 1 5 0 cm and 110 135
a B MI o 40. C alculate the minimum 50
amount o body mass she must lose to 100 140
95
reach normal body mass status. S how 90 40
145
all o your working. [3 ] 85
80 150
75 30
70 155
65
160
60 20
165
55
170
50
175
45
180
40
10 185

35 190
195
30 200
205
25 210

 Figure 10 Jogger  Figure 11

Fatty acids
Fatty acids can be saturated, monounsaturated or
polyunsaturated.
The basic structure o atty acids was described in sub- topic 2 .1 . There is
a chain o carbon atoms, with hydrogen atoms linked to them by single
covalent bonds. It is thereore a hydrocarbon chain. At one end o the
chain is the acid part o the molecule. This is a carboxyl group, which
can be represented as C O O H.
The length o the hydrocarbon chain is variable but most o the atty acids
used by living organisms have between 1 4 and 20 carbon atoms. Another
variable eature is the bonding between the carbon atoms. In some atty

81
2 M O L E C U L AR B I O LO G Y

O OH acids all o the carbon atoms are linked by single covalent bonds,
C but in other atty acids there are one or more positions in the chain
O OH H C H O OH where carbon atoms are linked by double covalent bonds.
C H C H C
I a carbon atom is linked to adj acent carbons in the chain by single
H C H H C H H C H bonds, it can also bond to two hydrogen atoms. I a carbon atom
H C H H C H H C H is linked by a double bond to an adj acent carbon in the chain,
H C H H C H H C H it can only bond to one hydrogen atom. A atty acid with single
H C H H C H H C H bonds between all o its carbon atoms thereore contains as much
H C H H C H H C H hydrogen as it possibly could and is called a saturated fatty acid.
H C H C H H C H Fatty acids that have one or more double bonds are unsaturated
H C H C H H C H because they contain less hydrogen than they could. I there is
H C H H C H C H one double bond, the atty acid is monounsaturated and i it has
H C H C H C H more than one double bond it is p olyunsaturated.
H C H C H H C H Figure 1 2 shows one saturated atty acid, one monounsaturated
H C H H C H H C H and one polyunsaturated atty acid. It is not necessary to remember
H C H C H H C H names o specifc atty acids in IB B iology.
H C H C H H C H
H C H H C H H C H
H C H H C H H C H
unsatrated fatty acids
H H H Unsaturated fatty acids can be cis or trans isomers.
palmitic acid linolenic acid palmitoleic acid In unsaturated atty acids in living organisms, the hydrogen atoms
 saturated  polyunsaturated  monounsaturated are nearly always on the same side o the two carbon atoms that
 non-essential  all cis  cis are double bonded  these are called cis- atty acids. The alternative
 essential  non-essential is or the hydrogens to be on opposite sides  called trans- atty
 omega 3  omega 7
acids. These two conormations are shown in fgure 1 4.
 Figure 12 Examples of fatty acids
In cis-atty acids, there is a bend in the hydrocarbon chain at the
double bond. This makes triglycerides containing cis- unsaturated
atty acids less good at packing together in regular arrays than
saturated atty acids, so it lowers the melting point. Triglycerides
with cis- unsaturated atty acids are thereore usually liquid at room
temperature  they are oils.
Trans-atty acids do not have a bend in the hydrocarbon chain at
the double bond, so they have a higher melting point and are solid
at room temperature. Trans-atty acids are produced artifcially by
partial hydrogenation o vegetable or fsh oils. This is done to produce
solid ats or use in margarine and some other processed oods.

H H H
C C C C
cis H
trans
 Figure 13 Double bonds
in fatty acids  Figure 14 Fatty acid stereochemistry  (a) trans (b) cis

82
2 . 3 c a r b o h y d r at e s a n d l i P i d s

Health risks of fats


Scientifc evidence or health risks o trans-ats and
saturated ats.
There have been many claims about the eects o dierent types o at
on human health. The main concern is coronary heart disease ( C HD ) .
In this disease the coronary arteries become partially blocked by atty
deposits, leading to blood clot ormation and heart attacks.
A positive correlation has been ound between saturated atty acid
intake and rates o C HD in many research programs. However, fnding
a correlation does not prove that saturated ats cause the disease. It
could be another actor correlated with saturated at intake, such as
low amounts o dietary fbre, that actually causes C HD .
There are populations that do not ft the correlation. The Maasai o
Kenya or example have a diet that is rich in meat, at, blood and  Figure 15 Triglycerides inolive oil
milk. They thereore have a high consumption o saturated ats, contain cis-unsaturated fatty acids
yet C HD is almost unknown among the Maasai. Figure 1 7 shows
members o another Kenyan tribe that show this trend.
D iets rich in olive oil, which contains cis- monounsaturated atty acids,
are traditionally eaten in countries around the Mediterranean. The
populations o these countries typically have low rates o C HD and it
has been claimed that this is due to the intake o cis- monounsaturated
atty acids. However, genetic actors in these populations, or other
aspects o the diet such as the use o tomatoes in many dishes could
explain the C HD rates.
There is also a positive correlation between amounts o trans-at
consumed and rates o C HD . Other risk actors have been tested, to
see i they can account or the correlation, but none did. Trans-ats
thereore probably do cause C HD . In patients who had died rom C HD , narrowed fatty plaque causing
atty deposits in the diseased arteries have been ound to contain high lumen of artery thickening of the artery lining
concentrations o trans-ats, which gives more evidence o a causal link.

layer of muscle outer coat of artery


and elastic bres
 Figure 16 Artery showing fatty plaque

 Figure 17 Samburu people of Northern Kenya. Like the Maasai, the Samburu have
a diet rich in animal products but rates of heart disease are extremely low
83
2 M O L E C U L AR B I O LO G Y

evaluating th halth risks of foods


Evaluating claims: health claims made about lipids need to be assessed.
Many health claims about oods are made. In similar controlled experiments with humans. It
some cases the claim is that the ood has a health might be possible to select matched groups o
benet and in other cases it is that the ood is experimental subj ects in terms o age, sex and
harmul. Many claims have been ound to be alse health, but unless identical twins were used they
when they are tested scientically. would be genetically dierent. It would also be
almost impossible to control other variables such
It is relatively easy to test claims about the eects
as exercise and ew humans would be willing
o diet on health using laboratory animals. Large
to eat a very strictly controlled diet or a long
numbers o genetically uniorm animals can be bred
enough period.
and groups o them with the same age, sex and state
o health can be selected or use in experiments. Researchers into the health risks o ood must
Variables other than diet, such as temperature and thereore use a dierent approach. Evidence is
amount o exercise, can be controlled so that they obtained by epidemiological studies. These involve
do not infuence the results o the experiment. Diets nding a large cohort o people, measuring their
can be designed so that only one dietary actor varies ood intake and ollowing their health over a
and strong evidence can thus be obtained about the period o years. S tatistical procedures can then
eect o this actor on the animal. be used to nd out whether actors in the diet
are associated with an increased requency o a
Results o animal experiments are oten
particular disease. The analysis has to eliminate
interesting, but they do not tell us with certainty
the eects o other actors that could be causing
what the health eects are on humans o a actor
the disease.
in the diet. It would be very dicult to carry out

Nature of science question: using volunteers in experiments.


D uring the S econd World War, experiments humans, cannot synthesize ascorbic acid. D uring
were conducted both in England and in the US trial periods with various intakes o vitamin C ,
using conscientious obj ectors to military service concentrations in blood plasma and urine were
as volunteers. The volunteers were willing to monitored. The guinea- pigs were then killed and
sacrice their health to help extend medical collagen in bone and skin was tested. The collagen
knowledge. A vitamin C trial in E ngland involved in guinea- pigs with restricted vitamin C had less
2 0 volunteers. For six weeks they were all given cross- linking between the protein bres and
a diet containing 70 mg o vitamin C . Then, or thereore lower strength.
the next eight months, three volunteers were
1 Is it ethically acceptable or doctors or
kept on the diet with 70 mg, seven had their
scientists to perorm experiments on
dose reduced to 1 0 mg and ten were given no
volunteers, where there is a risk that the
vitamin C . All o these ten volunteers developed
health o the volunteers will be harmed?
scurvy. Three- centimetre cuts were made in
their thighs, with the wounds closed up with 2 S ometimes people are paid to participate in
ve stitches. These wounds ailed to heal. There medical experiments, such as drug trials. Is
was also bleeding rom hair ollicles and rom the this more or less acceptable than using unpaid
gums. S ome o the volunteers developed more volunteers?
serious heart problems. The groups given 1 0 mg 3 Is it better to use animals or experiments or are
or 70 mg o vitamin C ared equally well and did the ethical objections the same as with humans?
not develop scurvy.
4 Is it acceptable to kill animals, so that an
Experiments on requirements or vitamin C have experiment can be done?
also been done using real guinea- pigs, which
ironically are suitable because guinea-pigs, like

84
2 . 3 c a r b o h y d r at e s a n d l i P i d s

anlysis of dt on helth risks of lipids


Evaluation of evidence and the methods used to obtain the evidence for health
claims made about lipids.
An evaluation is defned in IB as an assessment o  How widely spread is the data? This is shown
implications and limitations. Evidence or health by the spread o data points on a scattergraph
claims comes rom scientifc research. There are or the size o error bars on a bar chart. The
two questions to ask about this research: more widely spread the data, the less likely it
is that mean dierences are signifcant.
1 Implications  do the results o the research
support the health claim strongly, moderately  I statistical tests have been done on the data,
or not at all? do they show signifcant dierences?
2 Limitations  were the research methods used The second question is answered by assessing the
rigorous, or are there uncertainties about methods used. The points below reer to surveys
the conclusions because o weaknesses in and slightly dierent questions should be asked to
methodology? assess controlled experiments.
The frst question is answered by analysing the  How large was the sample size? In surveys it is
results o the research  either experimental usually necessary to have thousands o people
results or results o a survey. Analysis is usually in a survey to get reliable results.
easiest i the results are presented as a graph or  How even was the sample in sex, age, state o
other type o visual display.
health and lie style? The more even the sample,
 Is there a correlation between intake o the the less other actors can aect the results.
lipid being investigated and rate o the disease  I the sample was uneven, were the results
or the health beneft? This might be either a
adjusted to eliminate the eects o other actors?
positive or negative correlation.
 Were the measurements o lipid intake and
 How large is the dierence between mean
disease rates reliable? S ometimes people in a
( average) rates o the disease with dierent
survey do not report their intake accurately
levels o lipid intake? Small dierences may
and diseases are sometimes misdiagnosed.
not be signifcant.

d- qu: Evaluating evidence from a health survey


The Nurses Health S urvey is a highly respected Health Study. American Journal of Epidemiology,
survey into the health consequences o many 1 61 :672 679. doi:1 0.1 093 /aj e/kwi085
actors. It began in 1 976 with 1 2 1 , 700 emale
To asse ss the eects o trans- ats on rates
nurses in the US A and C anada, who completed a
o C HD , the participants in the survey were
lengthy questionnaire about their liestyle actors
divide d into ive groups according to the ir
and medical history. Follow- up questionnaires
trans- at intake. Q uintile 1 was the 2 0 % o
have been completed every two years since then.
participants with the lowest intake and quintile
D etails o the methods used to assess diet and 5 was the 2 0 % with the highe st intake. The
diagnose coronary heart disease can be ound ave rage intake o trans- ats or each quintile
by reading a research paper in the American was calculated, as a percentage o dietary
Journal o Epidemiology, which is reely available energy intake. The re lative risk o C HD was
on the internet: O h, K, Hu, FB , Manson, JE, o und or each quintile, with Q uintile 1
S tamper, MJ and Willett, WC . ( 2 005 ) D ietary assigned a risk o 1 . The risk was adj usted or
Fat Intake and Risk o C oronary Heart D isease die rences b etween the quintiles in age , body
in Women: 2 0 Years o Follow-up o the Nurses mass index, smoking, alcohol intake , parental

85
2 M O L E C U L AR B I O LO G Y

history o C HD , intake o other oods that 1.6


aect C HD rate s and various othe r actors. 1.4
Figure 1 8 is a graph showing the percentage 1.2

relative risk of CHD


o ene rgy rom trans- ats or e ach o the ive
1.0
quintiles and the adj uste d relative risk o
0.8
C HD . The e e ct o trans- at intake on relative
risk o C HD is statistically signiicant with a 0.6
conidence level o  9 9 % . 0.4
0.2
1 S uggest reasons or using only emale nurses
in this survey. [3 ] 0
1 1.5 2.0 2.5 3.0
2 S tate the trend shown in the graph. [1 ] percentage of energy from trans-fats

3 The mean age o nurses in the fve quintiles Data for graph
was not the same. E xplain the reasons or % of energy from
adj usting the results to compensate or the trans-fat 1.3 1.6 1.9 2.2 2.8
eects o age dierences. [2 ] Relative risk of 1.0 1.08 1.29 1.19 1.33
4 C alculate the chance, based on the statistical CHD
tests, o the dierences in C HD risk being due
 Figure 18
to actors other than
trans- at intake. [2 ]
5 D iscuss evidence rom the graph that other
actors were
having some eect on rates o C HD . [2 ]

data-base questions: Saturated fats and coronary heart disease


Populations
Montegiorgio

Tanushimaru
ranked
W. Finland
E. Finland

Ushibuka
Crevalcor

Zrenjanin
Belgrade

Dalmatia
Slavonia
Zutphen

by % calories as
Velika

Rome
Crete

Corfu
USA

saturated fat

% Calories as
22 19 19 18 14 12 10 10 9 9 9 9 8 7 3 3
saturated fat
Death CHD
992 351 420 574 214 288 248 152 86 9 150 80 290 144 66 88
rate/
100,000 All
yr 1 causes 1727 1318 1175 1088 1477 509 1241 1101 758 543 1080 1078 1027 764 1248 1006

 Table 2

1 a) Plot a scattergraph o the data in table 2 . [5 ]


b) O utline the trend shown by the scattergraph. [2 ]
2 C ompare the results or:
a) E ast and West Finland; [2 ]
b) C rete and Montegiorgio. [2 ]
3 Evaluate the evidence rom this survey or saturated ats as a cause o coronary heart disease. [4]

86
2 .4 Protein s

2.4 P
understnding applictions
 Amino acids are linked together by
 Rubisco, insulin, immunoglobulins, rhodopsin,
condensation to orm polypeptides. collagen and spider silk as examples o the
 There are twenty diferent amino acids in range o protein unctions.
polypeptides synthesized on ribosomes.  Denaturation o proteins by heat or deviation o
 Amino acids can be linked together in any pH rom the optimum.
sequence giving a huge range o possible
polypeptides.
 The amino acid sequence o polypeptides is Skills
coded or by genes.
 Draw molecular diagrams to show the ormation
 A protein may consist o a single polypeptide or o a peptide bond.
more than one polypeptide linked together.
 The amino acid sequence determines the three-
dimensional conormation o a protein. Ntre of science
 Living organisms synthesize many diferent  Patterns, trends and discrepancies: most but
proteins with a wide range o unctions. not all organisms assemble polypeptides rom
 Every individual has a unique proteome. the same amino acids.

amino cids nd polypeptides


Amino acids are linked together by condensation to orm
polypeptides.
Polypeptides are chains of amino acids that are made by linking together
amino acids by condensation reactions. This happens on ribosomes by
a process called translation, which will be described in sub- topic 2 .7.
Polypeptides are the main component of proteins and in many proteins
they are the only component. S ome proteins contain one polypeptide
and other proteins contain two or more.
The condensation reaction involves the amine group (- NH 2 ) of one amino
acid and the carboxyl group (- C OOH) of another. Water is eliminated, as
peptide bond
carboxyl amino
group group
H H condensation H O H H
H O H O H O
(water removed)
N C C 1 N C C N C C N C C
H OH H OH H OH
R R R R
amino acid amino acid
H2O
 Figure 1 Condensation joins two amino acids with a peptide bond
87
2 M O L E C U L AR B I O LO G Y

in all condensation reactions, and a new bond is ormed between the two
amino acids, called a peptide bond. A dipeptide is a molecule consisting
o two amino acids linked by a peptide bond. A polypeptide is a molecule
consisting o many amino acids linked by peptide bonds.
Polypeptides can contain any number o amino acids, though chains
o ewer than 2 0 amino acids are usually reerred to as oligopeptides
rather than polypeptides. Insulin is a small protein that contains two
polypeptides, one with 2 1 amino acids and the other with 3 0. The largest
polypeptide discovered so ar is titin, which is part o the structure o
muscle. In humans titin is a chain o 3 4, 3 5 0 amino acids, but in mice it is
even longer with 3 5 , 2 1 3 amino acids.

Drawing peptide bonds


Draw molecular diagrams to show the ormation o a peptide bond.
To orm a dipeptide, two amino acids are linked by  There is chain o atoms linked by single covalent
a condensation reaction between the amine group bonds orming the backbone o the oligopeptide,
o one amino acid and the carboxyl group o the with a repeating sequence o - N- C- C-
other. This is shown in fgure 1 .  A hydrogen atom is linked by a single bond
The peptide bond is the same, whatever R to each nitrogen atom in the backbone and
group the amino acid carries. To test your skill an oxygen atom is linked by a double bond to
at showing how peptide bonds are ormed, try one o the two carbon atoms.
showing the ormation o a peptide bond between  The amine ( - NH 2 ) and carboxyl ( - C O O H)
two o the amino acids in fgure 2 . There are
groups are used up in orming the peptide
sixteen possible dipeptides that can be produced
bond and only remain at the ends o the
rom these our amino acids.
chain. These are called the amino and carboxyl
You could also try to draw an oligopeptide o our terminals o the chain.
amino acids, linked by three peptide bonds. I you  The R groups o each amino acid remain and
do this correctly, you should see these eatures:
proj ect outwards rom the backbone.
COOH
OH H C H H
H C H H C H H C H H
H 2 N C COOH H 2 N C COOH H 2 N C COOH H 2N C COOH
H H H H
serine glutamic acid alanine glycine

 Figure 2 Some common amino acids

The diversity of amino acids


There are twenty diferent amino acids in polypeptides
synthesized on ribosomes.
The amino acids that are linked together by ribosomes to make
polypeptides all have some identical structural eatures: a carbon atom
in the centre o the molecule is bonded to an amine group, a carboxyl
group and a hydrogen atom. The carbon atom is also bonded to an R
group, which is dierent in each amino acid.

88
2 .4 Protein s

Twenty dierent amino acids are used by ribosomes to make


polypeptides. The amine groups and the carboxyl groups are used up in
orming the peptide bond, so it is the R groups o the amino acids that
give a polypeptide its character. The repertoire o R groups allows living
organisms to make and use an amazingly wide range o proteins. Some
o the dierences are shown in table 1 . It is not necessary to try to learn
these specifc dierences but it is important to remember that because
o the dierences between their R groups, the twenty amino acids are
chemically very diverse.
S ome proteins contain amino acids that are not in the basic repertoire
o twenty. In most cases this is due to one o the twenty being modifed
acvy
ater a polypeptide has been synthesized. There is an example o scuvy
modifcation o amino acids in collagen, a structural protein used to Ascorbic acid (vitamin C) is
provide tensile strength in tendons, ligaments, skin and blood vessel needed to convert proline
walls. C ollagen polypeptides made by ribosomes contain proline into hydroxyproline, so
at many positions, but at some o these positions it is converted to ascorbic acid deciency
hydroxyproline, which makes the collagen more stable. leads to abnormal collagen
production. From your
Nine R groups are hydrophobic Eleven R groups are hydrophilic knowledge o the role o
with between zero and nine
Seven R groups can become charged collagen, what efects do
carbon atoms Four
hydrophilic
you expect this to have?
Four R groups act as Three R groups act as
Three R Six R groups R groups are an acid by giving up a a base by accepting a Test your predictions by
groups contain do not contain polar but never proton and becoming proton and becoming researching the symptoms
rings rings charged negatively charged positively charged o ascorbic acid deciency
(scurvy) .
 Table 1 Classifcation o amino acids

amino cids nd origins


Patterns, trends and discrepancies: most but not all organisms assemble
polypeptides rom the same amino acids.
It is a remarkable act that most organisms make will always avour organisms that use them
proteins using the same 2 0 amino acids. In some and do not use other amino acids.
cases amino acids are modifed ater a polypeptide  All lie has evolved rom a single ancestral
has been synthesized, but the initial process o
species, which used these 2 0 amino acids.
linking together amino acids on ribosomes with
B ecause o the way that polypeptides are
peptide bonds usually involves the same 2 0
made by ribosomes, it is difcult or any
amino acids.
organism to change the repertoire o amino
We can exclude the possibility that this trend is acids, either by removing existing ones or
due to chance. There must be one or more reasons adding new ones.
or it. S everal hypotheses have been proposed:
B iology is a complicated science and discrepancies
 These 20 amino acids were the ones produced are commonly encountered. Some species have
by chemical processes on Earth beore the origin been ound that use one o the three codons that
o lie, so all organisms used them and have normally signal the end o polypeptide synthesis
continued to use them. Other amino acids might ( stop codons) to encode an extra non- standard
have been used, i they had been available. amino acid. For example, some species use UGA
to code or selenocysteine and some use UAG to
 They are the ideal 2 0 amino acids or making
code or pyrrolysine.
a wide range o proteins, so natural selection

89
2 M O L E C U L AR B I O LO G Y

dt-bse questios: Commonality of amino acids


1 a) D iscuss which o the three hypotheses or use o the same
2 0 amino acids by most organisms is supported by the
evidence. [3 ]
b) S uggest ways o testing one o the hypotheses. [2 ]
2 C ell walls o bacteria contain peptidoglycan, a complex carbon
compound that contains sugars and short chains o amino acids.
Some o these amino acids are dierent rom the usual repertoire
o 2 0. Also, some o them are right-handed orms o amino acids,
whereas the 2 0 amino acids made into polypeptides are always the
 Figure 3 Kohoutek Comet  26 diferent let-handed orms. D iscuss whether this is a signifcant discrepancy
amino acids were ound in an articial comet
that alsifes the theory that living organisms all make polypeptides
produced by researchers at the Institut
using the same 2 0 amino acids. [5 ]
dAstrophysique Spatiale (CNRS/France) ,
which suggests that amino acids used by the
rst living organisms on Earth may have come
rom space Polypeptide diversity
Amino acids can be linked together in any sequence
ativity giving a huge range of possible polypeptides.
clultig polypeptie iversity Ribosomes link amino acids together one at a time, until a polypeptide is
ully ormed. The ribosome can make peptide bonds between any pair o
number number of possible amino acids, so any sequence o amino acids is possible.
of mio mio i sequees
The number o possible amino acid sequences can be calculated starting
is
with dipeptides ( table 2 ) . B oth amino acids in a dipeptide can be any
1 20 1 o the twenty so there are twenty times twenty possible sequences
2 20 2 400 ( 2 0 2 ) . There are 2 0  2 0  2 0 possible tripeptide sequences ( 2 0 3 ) . For
a polypeptide o n amino acids there are 2 0 n possible sequences.
3 8,000
The number o amino acids in a polypeptide can be anything rom 2 0 to
4 tens o thousands. Taking one example, i a polypeptide has 400 amino
20 6 64 million acids, there are 2 0 400 possible amino acid sequences. This is a mind-
bogglingly large number and some online calculators simply express it as
10.24 trillion
infnity. I we add all the possible sequences or other numbers o amino
 Table 2 Calculate the missing values acids, the number is eectively infnite.

Genes and polypeptides


The amino acid sequence of polypeptides is coded for
by genes.
The number o amino acid sequences that could be produced is
immense, but living organisms only actually produce a small raction o
these. Even so, a typical cell produces polypeptides with thousands o
dierent sequences and must store the inormation needed to do this.
The amino acid sequence o each polypeptide is stored in a coded orm
in the base sequence o a gene.
S ome genes have other roles, but most genes in a cell store the amino
 Figure 4 Lysozyme with nitrogen o amine acid sequence o a polypeptide. They use the genetic code to do this.
groups shown blue, oxygen red and sulphur Three bases o the gene are needed to code or each amino acid in
yellow. The active site is the clet upper let the polypeptide. In theory a polypeptide with 400 amino acids should
require a gene with a sequence o 1 , 2 00 bases. In practice genes are
90
2 .4 Protein s

always longer, with extra base sequences at both ends and sometimes
also at certain points in the middle.
The base sequence that actually codes for a polypeptide is known to
molecular biologists as the open reading frame. O ne puzzle is that
open reading frames only occupy a small proportion of the total D NA
of a species.

Proteins and polypeptides


A protein may consist o a single polypeptide or more than
one polypeptide linked together.
S ome proteins are single polypeptides, but others are composed of two
or more polypeptides linked together.  Figure 5 Integrin embedded in a membrane
Integrin is a membrane protein with two polypeptides, each of which (grey) shown olded and inactive and open
with binding sites inside and outside the cell
has a hydrophobic portion embedded in the membrane. Rather like the
indicated (red and purple)
blade and handle of a folding knife the two polypeptides can either be
adj acent to each other or can unfold and move apart when it is working.
C ollagen consists of three long polypeptides wound together to form
a rope- like molecule. This structure has greater tensile strength than acvy
the three polypeptides would if they were separate. The winding Molecular biologists are
allows a small amount of stretching, reducing the chance of the investigating the numbers o
molecule breaking. open reading rames in selected
Hemoglobin consists of four polypeptides with associated non-polypeptide species or each o the major
structures. The four parts of hemoglobin interact to transport oxygen groups o living organism. It is
more effectively to tissues that need it than if they were separate. still ar rom certain how many
genes in each species code or
num f a polypeptide that the organism
exmpl bckgud actually uses, but we can
plyppd
compare current best estimates:
Enzyme in secretions such as nasal mucus and
1 lysozyme tears; it kills some bacteria by digesting the  Drosophila melanogaster,
peptidoglycan in their cell walls. the ruit fy, has base
sequences or about 14,000
Membrane protein used to make connections polypeptides.
2 integrin
between structures inside and outside a cell.
 Caenorhabditis elegans, a
Structural protein in tendons, ligaments, skin
nematode worm with less
3 collagen and blood vessel walls; it provides high tensile
than a thousand cells, has
strength, with limited stretching.
about 19,000.
Transport protein in red blood cells; it binds
 Homo sapiens has base
4 hemoglobin oxygen in the lungs and releases it in tissues with
sequences or about 23,000
a reduced oxygen concentration.
dierent polypeptides.
 Table 3 Example o proteins with diferent numbers o polypeptides  Arabidopsis thaliana, a
small plant widely used in
research, has about 27,000.
Protein conformations
Can you nd any species with
The amino acid sequence determines the three-dimensional greater or lesser numbers o
conormation o a protein. open reading rames than these?
The conformation of a protein is its three-dimensional structure. The
conformation is determined by the amino acid sequence of a protein
and its constituent polypeptides. Fibrous proteins such as collagen
91
2 M O L E C U L AR B I O LO G Y

are elongated, usually with a repeating structure. Many proteins are


globular, with an intricate shape that oten includes parts that are helical
or sheet-like.
Amino acids are added one by one, to orm a polypeptide. They are
always added in the same sequence to make a particular polypeptide. In
globular proteins the polypeptides gradually old up as they are made,
to develop the fnal conormation. This is stabilized by bonds between
the R groups o the amino acids that have been brought together by
the olding.
In globular proteins that are soluble in water, there are hydrophilic
R groups on the outside o the molecule and there are usually
 Figure 6 Lysozyme, showing how a polypeptide
hydrophobic groups on the inside. In globular membrane proteins there
can be folded up to form a globular protein.
are regions with hydrophobic R groups on the outside o the molecule,
Three sections that are wound to form a helix
are shown red and a section that forms a sheet which are attracted to the hydrophobic centre o the membrane.
is shown yellow. Other parts of the polypeptide In fbrous proteins the amino acid sequence prevents olding up and
including both of its ends are green ensures that the chain o amino acids remains in an elongated orm.

Denaturation of proteins
Denaturation of proteins by heat or pH extremes.
The three- dimensional conormation o proteins E xtremes o pH, both acidic and alkaline, can
is stabilized by bonds or interactions between R cause denaturation. This is because charges on R
groups o amino acids within the molecule. Most groups are changed, breaking ionic bonds within
o these bonds and interactions are relatively the protein or causing new ionic bonds to orm.
weak and they can be disrupted or broken. This As with heat, the three-dimensional structure
results in a change to the conormation o the o the protein is altered and proteins that have
protein, which is called denaturation. been dissolved in water oten become insoluble.
There are exceptions: the contents o the stomach
A denatured protein does not normally return
are normally acidic, with a pH as low as 1 .5 , but
to its ormer structure  the denaturation is
this is the optimum pH or the protein-digesting
permanent. S oluble proteins oten become
enzyme pepsin that works in the stomach.
insoluble and orm a precipitate. This is due to
the hydrophobic R groups in the centre o the
molecule becoming exposed to the water around
by the change in conormation.
Heat can cause denaturation because it causes
vibrations within the molecule that can
break intermolecular bonds or interactions.
Proteins vary in their heat tolerance. S ome
microorganisms that live in volcanic springs or in
hot water near geothermal vents have proteins
that are not denatured by temperatures o 80 C
or higher. The best known example is D NA
polymerase rom Thermus aquaticus, a prokaryote
that was discovered in hot springs in Yellowstone
National Park. It works best at 80 C and because
o this it is widely used in biotechnology.
Nevertheless, heat causes denaturation o most  Figure 7 When eggs are heated, proteins that were dissolved
proteins at much lower temperatures. in both the white and the yolk are denatured. They become
insoluble so both yolk and white solidify

92
2 .4 Protein s

Protein functions
acvy
Living organisms synthesize many diferent proteins with du xpm
a wide range o unctions. A solution o egg albumen
O ther groups o carbon compounds have important roles in the cell, but in a test tube can be heated
none can compare with the versatility o proteins. They can be compared in a water bath to nd the
to the worker bees that perorm almost all the tasks in a hive. All o the temperature at which it
unctions listed here are carried out by proteins. denatures. The efects o pH
 C atalysis  there are thousands o dierent enzymes to catalyse
can be investigated by adding
specifc chemical reactions within the cell or outside it.
acids and alkalis to test tubes
o egg albumen solution.
 Muscle contraction  actin and myosin together cause the To quantiy the extent o
muscle contractions used in locomotion and transport around denaturation, a colorimeter
the body. can be used as denatured
 C ytoskeletons  tubulin is the subunit o microtubules albumen absorbs more light
that give animals cells their shape and pull on chromosomes than dissolved albumen.
during mitosis.
 Tensile strengthening  fbrous proteins give tensile strength
needed in skin, tendons, ligaments and blood vessel walls.
acvy
 B lood clotting  plasma proteins act as clotting actors that cause
bx
blood to turn rom a liquid to a gel in wounds.
Botox is a neurotoxin
 Transp ort of nutrients and gases  proteins in blood help
obtained rom Clostridium
transport oxygen, carbon dioxide, iron and lipids.
botulinum bacteria.
 C ell adhesion  membrane proteins cause adj acent animal cells 1 What are the reasons
to stick to each other within tissues. or injecting it into
 Membrane transp ort  membrane proteins are used or humans?
acilitated diusion and active transport, and also or electron 2 What is the reason or
transport during cell respiration and photosynthesis. Clostridium botulinum
 Hormones  some such as insulin, FS H and LH are proteins, producing it?
but hormones are chemically very diverse. 3 What are the reasons or
 Recep tors  binding sites in membranes and cytoplasm or injecting it rather than
hormones, neurotransmitters, tastes and smells, and also taking it orally?
receptors or light in the eye and in plants.
 Packing of D NA  histones are associated with D NA in eukaryotes
and help chromosomes to condense during mitosis.
 Immunity  this is the most diverse group o proteins, as cells can
make huge numbers o dierent antibodies.
There are many biotechnological uses or proteins including enzymes
or removing stains, monoclonal antibodies or pregnancy tests or
insulin or treating diabetics. Pharmaceutical companies now produce
many dierent proteins or treating diseases. These tend to be very
expensive, as it is still not easy to synthesize proteins artifcially.
Increasingly, genetically modifed organisms are being used as
microscopic protein actories.

93
2 M O L E C U L AR B I O LO G Y

exampls of protins
Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as
examples o the range o protein unctions.
Six proteins which illustrate some o the unctions o proteins are described in table 4.

rubo inuln
This name is an abbreviation or ribulose bisphosphate This hormone is produced as a signal to many cells in
carboxylase, which is arguably the most important the body to absorb glucose and help reduce the glucose
enzyme in the world. The shape and chemical properties concentration o the blood. These cells have a receptor
o its active site allow it to catalyse the reaction that xes or insulin in their cell membrane to which the hormone
carbon dioxide rom the atmosphere, which provides binds reversibly. The shape and chemical properties o
the source o carbon rom which all carbon compounds the insulin molecule correspond precisely to the binding
needed by living organisms can be produced. It is site on the receptor, so insulin binds to it, but not other
present at high concentrations in leaves and so is molecules. Insulin is secreted by  cells in the pancreas
probably the most abundant o all proteins on Earth. and is transported by the blood.

immunoglobuln rhodopn
These proteins are also known as antibodies. They have Vision depends on pigments that absorb light. One o
sites at the tips o their two arms that bind to antigens these pigments is rhodopsin, a membrane protein o rod
on bacteria or other pathogens. The other parts o the cells o the retina. Rhodopsin consists o a light sensitive
immunoglobulin cause a response, such as acting as a retinal molecule, not made o amino acids, surrounded
marker to phagocytes that can engul the pathogen. The by an opsin polypeptide. When the retinal molecule
binding sites are hypervariable. The body can produce absorbs a single photon o light, it changes shape. This
a huge range o immunoglobulins, each with a diferent causes a change to the opsin, which leads to the rod cell
type o binding site. This is the basis o specic immunity sending a nerve impulse to the brain. Even very low light
to disease. intensities can be detected.

collagen spde lk


There are a number o diferent orms o collagen but all Diferent types o silk with diferent unctions are
are rope-like proteins made o three polypeptides wound produced by spiders. Dragline silk is stronger than steel
together. About a quarter o all protein in the human body and tougher than Kevlar. It is used to make the spokes
is collagen  it is more abundant than any other protein. o spiders webs and the lielines on which spiders
It orms a mesh o bres in skin and in blood vessel suspend themselves. When rst made it contains
walls that resists tearing. Bundles o parallel collagen regions where the polypeptide orms parallel arrays.
molecules give ligaments and blood vessel walls their Other regions seem like a disordered tangle, but when
immense strength. It orms part o the structure o teeth the silk is stretched they gradually extend, making the
and bones, helping to prevent cracks and ractures. silk extensible and very resistant to breaking.

Protoms
Every individual has a unique proteome.
A proteome is all o the proteins produced by a cell, a tissue or an
organism. B y contrast, the genome is all o the genes o a cell, a tissue or
an organism. To fnd out how many dierent proteins are being produced,
mixtures o proteins are extracted rom a sample and are then separated

94
2 .4 Protein s

by gel electrophoresis. To identiy whether or not a particular protein is


present, antibodies to the protein that have been linked to a fuorescent
marker can be used. I the cell fuoresces, the protein is present.
Whereas the genome o an organism is xed, the proteome is variable
because dierent cells in an organism make dierent proteins. Even
in a single cell the proteins that are made vary over time depending
on the cells activities. The proteome thereore reveals what is actually
happening in an organism, not what potentially could happen.
Within a species there are strong similarities in the proteome o all
individuals, but also dierences. The proteome o each individual is
unique, partly because o dierences o activity but also because o small
dierences in the amino acid sequence o proteins. With the possible
exception o identical twins, none o us have identical proteins, so each
o us has a unique proteome. E ven the proteome o identical twins can
become dierent with age.

 Figure 8Proteins rom a nematode worm have been separated by gel


electrophoresis. Each spot on the gel is a diferent protein

acvy
acv cc: gm d pm
We might expect the proteome of an organism to be smaller than its genome,
as some genes do not code for polypeptides. In fact the proteome is larger.
How could an organism produce more proteins than the number of genes that
its genome contains?

95
2 M O L E C U L AR B I O LO G Y

2.5 enzyms
understnding applictions
 Enzymes have an active site to which specic
 Methods o production o lactose-ree milk and
substrates bind. its advantages.
 Enzyme catalysis involves molecular motion
and the collision o substrates with the
active site.
 Temperature, pH and substrate concentration
afect the rate o activity o enzymes.
 Enzymes can be denatured.
 Immobilized enzymes are widely used in
industry.

Ntre of science Skills


 Experimental design: accurate quantitative  Design o experiments to test the efect o
measurements in enzyme experiments require temperature, pH and substrate concentration
replicates to ensure reliability. on the activity o enzymes.
 Experimental investigation o a actor afecting
enzyme activity. (Practical 3)

active sites nd enzymes


Enzymes have an active site to which specic
substrates bind .
Enzymes are globular proteins that work as catalysts  they speed up
chemical reactions without being altered themselves. Enzymes are oten
called biological catalysts because they are made by living cells and speed
up biochemical reactions. The substances that enzymes convert into
products in these reactions are called substrates. A general equation or
an enzyme- catalysed reaction is:
e nzym e
substrate _______  product
Enzymes are ound in all living cells and are also secreted by some cells
to work outside. Living organisms produce many dierent enzymes 
literally thousands o them. Many dierent enzymes are needed, as
enzymes only catalyse one biochemical reaction and thousands o
 Figure 1 Computer-generated image of the reactions take place in cells, nearly all o which need to be catalysed.
enzyme hexokinase, with a molecule of its This property is called enzymesubstrate sp ecifcity. It is a signifcant
substrate glucose bound to the active site. The dierence between enzymes and non- biological catalysts such as the
enzyme bonds a second substrate, phosphate, metals that are used in catalytic converters o vehicles.
to the glucose, to make glucose phosphate
To be able to explain enzymesubstrate specifcity, we must look at the
mechanism by which enzymes speed up reactions. This involves the
96
2 . 5 en z yM e s

substrate, or substrates binding to a special region on the surace o the


enzyme called the active site (see fgure 1 ) . The shape and chemical
properties o the active site and the substrate match each other. This allows
the substrate to bind, but not other substances. Substrates are converted
into products while they are bound to the active site and the products are
then released, reeing the active site to catalyse another reaction.

data-ba qutio: Biosynthesis of glycogen


The Nobel Prize or Medicine was won in 1 947 by glycogen. Glycogen is a polysaccharide, composed
Gerty C ori and her husband C arl. They isolated o glucose molecules bonded together in two
two enzymes that convert glucose phosphate into ways, called 1 , 4 and 1 , 6 bonds ( see fgure 2 ) .
4 C urve B was obtained using enzymes that
had not been heat- treated.
a) D escribe the shape o C urve B . [2 ]
1 4 bonding 1 4 bonding plus a b) Explain the shape o C urve B . [2 ]
1 6 bond forming a side-branch

% conversion
 Figure 2 Bonding in glycogen 80 B

1 Explain why two dierent enzymes are 60


needed or the synthesis o glycogen
rom glucose phosphate. [2 ] 40

2 The ormation o side-branches increases the 20


rate at which glucose phosphate molecules A
can be linked on to a growing glycogen 10 20 30 40 50
min
molecule. Explain the reason or this. [2 ]
 Figure 3 shows the percentage conversion of glucose
3 C urve A was obtained using heat- treated phosphate to glycogen by the two enzymes, over a
enzymes. Explain the shape o curve A. [2 ] 50-minute period

enzym activity
Enzyme catalysis involves molecular motion and the
collision of substrates with the active site.
E nzyme activity is the catalysis o a reaction by an enzyme. There are
three stages:
 The substrate binds to the active site o the enzyme. S ome enzymes
have two substrates that bind to dierent parts o the active site.
 While the substrates are bound to the active site they change into
dierent chemical substances, which are the products o the reaction.
 The products separate rom the active site, leaving it vacant or
substrates to bind again.
A substrate molecule can only bind to the active site i it moves very
close to it. The coming together o a substrate molecule and an active
site is known as a collision. This might suggest a high velocity impact
between two vehicles on a road, but that would be a misleading image
and we need to think about molecular motion in liquids to understand
how substrateactive site collisions occur.
With most reactions the substrates are dissolved in water around
the enzyme. B ecause water is in a liquid state, its molecules and all
97
2 M O L E C U L AR B I O LO G Y

the particles dissolved in it are in contact with each other and are in
toK continual motion. E ach particle can move separately. The direction of
Why hs he lck nd key mdel movement repeatedly changes and is random, which is the basis of
n been lly superseded by he diffusion in liquids. B oth substrates and enzymes with active sites are
induced-f mdel? able to move, though most substrate molecules are smaller than the
enzyme so their movement is faster.
The lock and key model and the
induced-t model were both developed S o, collisions between substrate molecules and the active site occur
to help to explain enzyme activity. because of random movements of both substrate and enzyme. The
Models like these are simplied substrate may be at any angle to the active site when the collision
descriptions, which can be used to occurs. Successful collisions are ones in which the substrate and active
make predictions. Scientists test these site are correctly aligned to allow binding to take place.
predictions, usually by perorming
experiments. I the results agree
with the predictions, then the model
is retained; i not then the model is
water molecules
modied or replaced. The German
scientist Emil Fischer introduced the
lock and key model in 1890. Daniel
Koshland suggested the induced-t substrates
model in 1959 in the United States. The
conormational changes predicted by
Koshland's model were subsequently
observed using high-resolution X-ray
analysis o enzymes and other newly active site
developed techniques. Although
much experimental evidence has part of enzyme
accumulated conrming predictions
 Figure 4 Enzyme-substrate collisions. If random movements bring any of the substrate
based on the induced-t model, it is molecules close to the active site with the correct orientation, the substrate can bind to the
still just viewed as a model o enzyme active site
activity.

Factors afecting enzyme activity


Temperature, pH and substrate concentration afect the
aciviy rate o activity o enzymes.
Mking  hyphesis
Enzyme activity is afected by temperature in two ways
Bacillus licheniformis lives
 In liquids, the particles are in continual random motion. When a liquid is
in soil and on decomposing
heated, the particles in it are given more kinetic energy. Both enzyme and
eathers. What is the reason
substrate molecules therefore move around faster at higher temperatures
or it producing a protease
and the chance of a substrate molecule colliding with the active site of the
that works best at alkaline
enzyme is increased. Enzyme activity therefore increases.
pH? Make a hypothesis to
explain the observations.  When enzymes are heated, bonds in the enzyme vibrate more and
How could you test your the chance of the bonds breaking is increased. When bonds in the
hypothesis? enzyme break, the structure of the enzyme changes, including the
active site. This change is permanent and is called denaturation.
When an enzyme molecule has been denatured, it is no longer able
to catalyse reactions. As more and more enzyme molecules in a
solution become denatured, enzyme activity falls. Eventually it stops
altogether, when the enzyme has been completely denatured. So, as
temperature rises there are reasons for both increases and decreases
in enzyme activity. Figure 5 shows the effects of temperature on a
typical enzyme.
98
2 . 5 en z yM e s

Enzymes are sensitive to pH rate at which reaction decreases owing


to denaturation of enzyme molecules
The pH scale is used to measure the acidity or alkalinity o a solution.
The lower the pH, the more acid or the less alkaline a solution is. Acidity
is due to the presence o hydrogen ions, so the lower the pH, the higher
the hydrogen ion concentration. The pH scale is logarithmic. This means optimum

rate of reaction
rate at which
that reducing the pH by one unit makes a solution ten times more acidic. reaction increases temperature
A solution at pH 7 is neutral. A solution at pH 6 is slightly acidic; pH 5 is owing to increased
ten times more acidic than pH 6, pH 4 is one hundred times more acidic kinetic energy of
substrate and
than pH 6, and so on. enzyme
molecules
Most enzymes have an optimum pH at which their activity is actual
highest. I the pH is increased or decreased rom the optimum, rate of
enzyme activity decreases and eventually stops altogether. When reaction
the hydrogen ion concentration is higher or lower than the level at
0 10 20 30 40 50 60
which the enzyme naturally works, the structure o the enzyme is
temperature/C
altered, including the active site. B eyond a certain pH the structure
o the enzyme is irreversibly altered. This is another example o  Figure 5 Temperature and enzyme activity
denaturation.
E nzyme s do no t all have the same p H o p timu m  in act, the re is
a wide range . This re le cts the wide range o  p H e nviro nme nts in Key
which e nzyme s wo rk. Fo r e xamp le , the p ro te ase se cre te d b y Bacillus 1 stomach
lichen iform is has a p H o p timum b e twe e n 9 and 1 0 . This b acte rium acidic hot springs
2 decaying plant matter
is cu lture d to p ro duce its alkaline - to le rant p ro te ase o r u se in
large intestine
b io lo gical lau ndry de te rge nts, which are alkaline . Figure 6 sho ws 3
small intestine
the p H range o  so me o  the p lace s whe re e nzyme s wo rk. Figu re  7 alkaline lakes
4
sho ws the e e cts o  p H o n an e nzyme that is adap te d to wo rk at
ne u tral p H. 5

6
Enzyme activity is afected by substrate concentration
E nzymes cannot catalyse reactions until the substrate binds to the active 7
site. This happens because o the random movements o molecules in
8
liquids that result in collisions between substrates and active sites. I the
concentration o substrates is increased, substrateactive site collisions 9
will take place more requently and the rate at which the enzyme
10
catalyses its reaction increases.
However, there is another trend that needs to be
 Figure 6
considered. Ater the binding o a substrate to
an active site, the active site is occupied and
Optimum pH at which enzyme
unavailable to other substrate molecules until
activity is fastest (pH 7 is
products have been ormed and released rom the optimum for most enzymes) .
active site. As the substrate concentration rises,
more and more o the active sites are occupied at
any moment. A greater and greater proportion o As pH increases or decreases from the
substrateactive site collisions are thereore blocked. optimum, enzyme activity is reduced.
enzyme activity

This is because the shape of the active


For this reason, the increases in the rate at which
site is altered so the substrate does not
enzymes catalyse reactions get smaller and smaller t so well. Most enzymes are denatured
as substrate concentration rises. by very high or low pH, so the enzyme
no longer catalyses the reaction.
I the relationship between substrate concentration
and enzyme activity is plotted on a graph, a
distinctive curve is seen ( fgure 8) , rising less and pH
less steeply, but never quite reaching a maximum.  Figure 7 pH and enzyme activity

99
2 M O L E C U L AR B I O LO G Y

Denaturation
Enzymes can be denatured.
Enzymes are proteins, and like other proteins their structure can be
irreversibly altered by certain conditions. This process is denaturation
enzyme activity

and both high temperatures and either high or low pH can cause it.
When an enzyme has been denatured, the active site is altered so the
substrate can no longer bind, or i its binds, the reaction that the enzyme
normally catalyses does not occur. In many cases denaturation causes
enzymes that were dissolved in water to become insoluble and orm a
precipitate.
substrate concentration
 Figure 8 The efect o substrate
concentration on enzyme activity

Quantitative experiments
Experimental design: accurate quantitative measurements in enzyme
experiments require replicates to ensure reliability.
O ur understanding o enzyme activity is based  measurements should be accurate, which in
on evidence rom experiments. To obtain strong science means close to the true value; and
evidence these experiments must be careully  the experiment should be repeated, so that
designed and ollow some basic principles:
the replicate results can be compared to assess
 the results o the experiment should be how reliable they are.
quantitative, not j ust descriptive;

data-base questions: Digesting jello cubes


Figure 9 shows apparatus that can be used to a) describing whether the solution around the
investigate protein digestion. cubes is colourless or a shade o pink or red
b) taking a sample o the solution and
tube tight-tting lid
measuring its absorbance in a colorimeter
c) nding the mass o the cubes using an
electronic balance. [3 ]
2 I method ( c) was chosen, discuss whether it
would be better
protease in a solution gelatine cubes
with known pH to nd the mass o all o the cubes o j ello
together, or nd
 Figure 9 Tube used to investigate the rate o digestion o gelatine
the mass o each one separately. [2 ]
3 I the j ello cubes have a mass o 0.5 grams,
I the cubes are made rom sugar- ree j ello ( j elly) , state whether it is accurate enough to
the colouring that they contain will gradually be measure their mass to:
released as the protein is digested by the protease.
a) the nearest gram ( g)
The questions below assume that strawberry-
favoured j ello with red colouring has been used! b) the nearest milligram ( mg)
c) the nearest microgram ( g) . [3 ]
1 Explain whether these methods o assessing
the rate o protein digestion are acceptable:

100
2 . 5 en z yM e s

4 To obtain accurate mass measurements o 7 D raw a graph o the results in the table. [5 ]
the j ello cubes, it is necessary to remove 8 D escribe the relationship between pH and
them rom the tube and dry their surace papain activity. [3 ]
to ensure that there are no drips o solution
rom the tube adhering. Explain the reason 9 D iscuss the conclusions that can be drawn
or drying the surace o the blocks. [2 ] rom this data about the precise optimum
pH o papain. [2 ]
Table 1 gives the results that were obtained using
sugar-ree jello cubes and a protease called papain,
ph Ma dcra (mg)
extracted rom the fesh o resh pineapples.
2 80 87 77
5 D iscuss whether the results in table 1 are
reliable. [2 ] 3 122 127 131
6 Most o the results were obtained using an 4 163 166 164
extract o protease rom one pineapple, but 5 171 182 177
ater this ran out, a second pineapple was
used to obtain more protease or use in the 6 215 210 213
experiment. 7 167 163 84
a) Deduce which results were obtained 8 157 157 77
using the second extract. [1 ]
9 142 146 73
b) S uggest how the use o a second
extract could have aected the results. [2 ]  Table 1

Designing enzyme experiments


Design o experiments to test the efect o temperature, pH and substrate
concentration on the activity o enzymes.
1 The actor that you are going to investigate is the clock could be used to measure the time
independent variable. You need to decide: taken or a colour change;
 how you are going to vary it, or example  what units should be used or measuring
with substrate concentration you would the dependent variable, or example
obtain a solution with the highest seconds rather than minutes or hours
concentration and dilute it to get lower would be used or measuring a rapid
concentrations; colour change;
 what units should be used or measuring  how many repeats you need to get reliable
the independent variable, or example enough results.
temperature is measured in degrees C elsius; 3 Other actors that could aect the dependent are
 what range you need or the independent control variables. You need to decide:
variable, including the highest and lowest  what all the control variables are;
levels and the number o intermediate levels.  how each o them can be kept constant;
2 The variable that you measure to nd out how
 what level they should be kept at, or
ast the enzyme is catalysing the reaction is the
example temperature should be kept at
dependent variable. You need to decide:
the optimum or the enzyme i pH is being
 how you are going to measure it, including investigated, but actors that might inhibit
the choice o meter or other measuring enzymes should be kept at a minimum level.
device, or example an electronic stop

101
2 M O L E C U L AR B I O LO G Y

enzym xprimnts
Experimental investigation o a actor afecting enzyme activity.
There are many worthwhile enzyme experiments. constant i investigating the eect o
The method that ollows can be used to substrate concentration. [2 ]
investigate the eect o substrate concentration on
4 Predict whether the enzyme activity will
the activity o catalase.
change more i substrate concentration is
C atalase is one o the most widespread enzymes. increased by 0. 2 mol dm - 3 or i it is decreased
It catalyses the conversion o hydrogen peroxide, by the same amount. [2 ]
a toxic by- product o metabolism, into water and
5 Explain why tissues such as liver must be
oxygen. The apparatus shown in fgure 1 0 can be
macerated beore investigating catalase
used to investigate the activity o catalase in yeast.
activity in them. [2 ]
The experiment could be repeated using the same
Safety goggles must be worn if this experiment
concentration o yeast, but dierent hydrogen
is performed. Care should be taken not to get
peroxide concentrations. Another possible
hydrogen peroxide on the skin.
investigation would be to assess the catalase
concentrations in other cell types, such as liver,
kidney or germinating seeds. These tissues would oxygen
have to be macerated and then mixed with water
at the same concentration as the yeast. yeast measuring cylinder

1 D escribe how the activity o the enzyme three-way tap


water
catalase could be measured using the
apparatus shown in fgure 1 0. [2 ]
2 Explain why a yeast suspension must always
be thoroughly stirred beore a sample o it is water
0.8 mol dm 2 3
taken or use in an experiment. [2]
hydrogen peroxide
3 S tate two actors, apart rom enzyme
concentration, that should be kept  Figure 10 Apparatus for measuring catalase activity

 Figure 11 Enzyme experiment

102
2 . 5 en z yM e s

data-ba qutio: Designing an experiment to fnd the eect o temperature on lipase.


Lipase converts fats into fatty acids and glycerol. It 2 a) Explain how you would measure the
therefore causes a decrease in pH. This pH change dependent variable accurately. [2 ]
can be used to measure the activity of lipase.
b) S tate the units for measuring the
Figure 1 2 shows suitable apparatus.
dependent variable. [1 ]
tube contents mixed when both c) Explain the need for at least three
have reached target temperature replicate results for each temperature
in this experiment. [2 ]
thermometer 3 a) List the control factors that must be
kept constant in this experiment. [3 ]
b) Explain how these control factors can
be kept constant. [2 ]
c) S uggest a suitable level for each
control factor. [3 ]
4 S uggest reasons for:
a) milk being used to provide a source of
thermostatically lipase milk mixed with lipids in this experiment rather than
controlled sodium carbonate (an alkali)
water bath and phenolphthalein vegetable oil. [1 ]
(a pH indicator)
b) the thermometer being placed in the
 Figure 12 Apparatus for investigating the activity of lipase tube containing the larger, rather than
the smaller, volume of liquid [1 ]
Phenolphthalein is pink in alkaline conditions,
but becomes colourless when the pH drops to c) the substrate being added to the
7. The time taken for this colour change can be enzyme, rather than the enzyme to
used to measure the activity of lipase at different the substrate. [1 ]
temperatures. Alternatively, pH changes could
5 S ketch the shape of graph that you would
be followed using a pH probe and data- logging
expect from this experiment, with a
software.
temperature range from 0 C to 80 C on
1 a) State the independent variable in this the x- axis and time taken for the indicator
experiment and how you would vary it. [2 ] to change colour on the y- axis. [2 ]
b) S tate the units for measuring the 6 Explain whether lipase from human pancreas
independent variable. [1 ] or from germinating castor oil seeds would
be expected to have the higher optimum
c) State an appropriate range for the
temperature. [2 ]
independent variable. [2 ]

Immobilized enzymes
Immobilized enzymes are widely used in industry.
In 1 897 the B uchner brothers, Hans and E duard, showed that an
extract of yeast, containing no yeast cells, would convert sucrose into
alcohol. The door was opened to the use of enzymes to catalyse chemical
processes outside living cells.
Louis Pasteur had claimed that fermentation of sugars to alcohol could
only occur if living cells were present. This was part of the theory of

103
2 M O L E C U L AR B I O LO G Y

vitalism, which stated that substances in animals and plants can only
toK be made under the infuence o a vital spirit or vital orce. The
Wha is he diference beween articial synthesis o urea, described in sub- topic 2 . 1 , had provided
dgma and hery? evidence against vitalism, but the B uchners research provided a clearer
alsication o the theory.
Ater the discovery in the 19th century
o the conversion o sugar into alcohol More than 5 00 enzymes now have commercial uses. Figure 1 3 shows a
by yeast, a dispute developed between classication o commercially useul enzymes. Some enzymes are used in
two scientists, Justus von Liebig and more than one type o industry.
Louis Pasteur. In 1860 Pasteur argued
that this process, called ermentation, miscellaneous 4% other industries 5%
could not occur unless live yeast cells agriculture 11%
were present. Liebig claimed that
the process was chemical and that
living cells were not needed. Pasteurs
view refected the vitalistic dogma  medical 21%
that the substances in animals and
plants could only be made under the biosensor 16%
infuence o a vital spirit or vital
orce. These contrasting views were food & nutrition 23%
as much infuenced by political and
religious actors as by scientic
biotechnology 46%
evidence. The dispute was only
resolved ater the death o both men.
In 1897 the Buchner brothers, Hans environment 13%
and Eduard, showed that an extract o
yeast, containing no yeast cells, did
indeed convert sucrose into alcohol. energy 3%
The vitalistic dogma was overthrown  Figure 13
and the door was opened to the use
o enzymes to catalyse chemical The enzymes used in industry are usually immobilized. This is
processes outside living cells. attachment o the enzymes to another material or into aggregations,
so that movement o the enzyme is restricted. There are many ways o
doing this, including attaching the enzymes to a glass surace, trapping
them in an alginate gel, or bonding them together to orm enzyme
aggregates o up to 0. 1 mm diameter.
Enzyme immobilization has several advantages.
 The enzyme can easily be separated rom the products o the
reaction, stopping the reaction at the ideal time and preventing
contamination o the products.
 Ater being retrieved rom the reaction mixture the enzyme may be
recycled, giving useul cost savings, especially as many enzymes are
very expensive.
 Immobilization increases the stability o enzymes to changes in
temperature and pH, reducing the rate at which they are degraded
and have to be replaced.
 S ubstrates can be exposed to higher enzyme concentrations than
with dissolved enzymes, speeding up reaction rates.

104
2 . 6 s tru ctu r e o f d n a an d r n a

lctose-free mik
Methods o production o lactose-ree milk and its advantages.
Lactose is the sugar that is naturally present in milk.  Lactose tends to crystallize during the
It can be converted into glucose and galactose by the production o ice cream, giving a gritty
enzyme lactase: lactose  glucose + galactose. texture. B ecause glucose and galactose
are more soluble than lactose they remain
Lactase is obtained rom Kluveromyces lactis,
dissolved, giving a smoother texture.
a type o yeast that grows naturally in milk.
B iotechnology companies culture the yeast,  B acteria erment glucose and galactose more
extract the lactase rom the yeast and puriy quickly than lactose, so the production o
it or sale to ood manuacturing companies. yoghurt and cottage cheese is aster.
There are several reasons or using lactase in
Thailand
ood processing:
South India
 S ome people are lactose-intolerant and cannot Crete
drink more than about 2 5 0 ml o milk per day, France
unless it is lactose- reduced ( see fgure 1 4) .
Finland
 Galactose and glucose are sweeter than Sweden
lactose, so less sugar needs to be added to 0% 50% 100%
sweet oods containing milk, such as milk lactose intolerance
shakes or ruit yoghurt.  Figure 14 Rates of lactose intolerance

2.6 s  dna  rna


understnding appictions
 The nucleic acids DNA and RNA are polymers o
 Crick and Watsons elucidation o the structure
nucleotides. o DNA using model-making.
 DNA difers rom RNA in the number o strands
normally present, the base composition and
the type o pentose.
 DNA is a double helix made o two antiparallel
strands o nucleotides linked by hydrogen
bonding between complementary base pairs.

Ntre of science Skis


 Using models as representation o the real  Drawing simple diagrams o the structure o
world: Crick and Watson used model-making to single nucleotides and o DNA and RNA, using
discover the structure o DNA. circles, pentagons and rectangles to represent
phosphates, pentoses and bases.

105
2 M O L E C U L AR B I O LO G Y

Nucleic cids nd nucleotides


The nucleic acids DNA and RNA are polymers o
nucleotides.
phosphate sugar base Nucleic acids were frst discovered in material extracted rom the nuclei
o cells, hence their name. There are two types o nucleic acid: D NA
O
and RNA. Nucleic acids are very large molecules that are constructed by
O P O CH 2 linking together nucleotides to orm a polymer.
5
O 1
O Nucleotides consist o three parts:
C C N
4

C3 2
C  a sugar, which has fve carbon atoms, so is a pentose sugar;
OH OH  a p hosp hate group, which is the acidic, negatively- charged part o
nucleic acids; and
 Figure 1 The parts of a nucleotide
 a base that contains nitrogen and has either one or two rings o
atoms in its structure.
Figure 1 shows these parts and how they are linked together. The base
and the phosphate are both linked by covalent bonds to the pentose
sugar. Figure 2 shows a nucleotide in symbolic orm.
To link nucleotides together into a chain or polymer, covalent bonds are
ormed between the phosphate o one nucleotide and the pentose sugar
o the next nucleotide. This creates a strong backbone or the molecule o
alternating sugar and phosphate groups, with a base linked to each sugar.
There are our dierent bases in both D NA and RNA, so there are our
dierent nucleotides. The our dierent nucleotides can be linked
 Figure 2 A simpler representation of a together in any sequence, because the phosphate and sugar used to link
nucleotide them are the same in every nucleotide. Any base sequence is thereore
possible along a D NA or RNA molecule. This is the key to nucleic acids
acting as a store o genetic inormation  the base sequence is the store
o inormation and the sugar phosphate backbone ensures that the store
is stable and secure.

Difeences between DNa nd rNa


DNA difers rom RNA in the number o strands normally
present, the base composition and the type o pentose.
HOH 2 C O OH
There are three important dierences between the two types o nucleic
H H acid:
H H 1 The sugar within D NA is deoxyribose and the sugar in RNA is ribose.
OH H Figure 3 shows that deoxyribose has one ewer oxygen atom than
ribose. The ull names o D NA and RNA are based on the type o
HOH 2 C O OH sugar in them  deoxyribonucleic acid and ribonucleic acid.

H H 2 There are usually two polymers o nucleotides in D NA but only one


in RNA. The polymers are oten reerred to as strands, so D NA is
H H double- stranded and RNA is single-stranded.
OH OH
3 The our bases in D NA are adenine, cytosine, guanine and
 Figure 3 The sugar within DNA is thymine. The our bases in RNA are adenine, cytosine, guanine
deoxyribose (top) and the sugar in and uracil, so the dierence is that uracil is present instead o
RNA is ribose (bottom)
thymine in RNA.

106
2 . 6 s tru ctu r e o f d n a an d r n a

d-b qi: Chargafs data


D NA samples from a range of species were 3 E valuate the claim that in the D NA of
analysed in terms of their nucleotide composition eukaryotes and prokaryotes the amount
by Edwin C hargaff, an Austrian biochemist, and of adenine and thymine are equal and
by others. The data is presented in table 1 . the amounts of guanine and cytosine
are equal. [2 ]
1 C ompare the base composition of
Mycobacterium tuberculosis ( a prokaryote) 4 E xplain the ratios between the amounts
with the base composition of the eukaryotes of bases in eukaryotes and prokaryotes in
shown in the table. [2 ] terms of the structure of D NA. [2 ]
2 C alculate the base ratio A+ G/T + C , for 5 S uggest reasons for the difference in the
humans and for Mycobacterium tuberculosis. base composition of bacteriophage T2 and
S how your working. [2 ] the polio virus. [2 ]

s  dna Gp ai Gi cyi thymi


Human Mammal 31.0 19.1 18.4 31.5
Cattle Mammal 28.7 22.2 22.0 27.2
Salmon Fish 29.7 20.8 20.4 29.1
Sea urchin Invertebrate 32.8 17.7 17.4 32.1
Wheat Plant 27.3 22.7 22.8 27.1
Yeast Fungus 31.3 18.7 17.1 32.9
Mycobacterium tuberculosis Bacterium 15.1 34.9 35.4 14.6
Bacteriophage T2 Virus 32.6 18.2 16.6 32.6
Polio virus Virus 30.4 25.4 19.5 0.0
 Table 1

Dwing DNa nd rNa molecules


Drawing simple diagrams of the structure of single
nucleotides and of DNA and RNA, using circles,
pentagons and rectangles to represent phosphates,
pentoses and bases.
The structure of D NA and RNA molecules can be shown in diagrams
using simple symbols for the subunits:
 circles for phosphates;
 pentagons for pentose sugar;
 rectangles for bases.
Figure 2 shows the structure of a nucleotide, using these symbols. The
base and the phosphate are linked to the pentose sugar. The base is
linked to C 1  the carbon atom on the right hand side of the pentose
sugar. The phosphate is linked to C 5  the carbon atom on the side
 Figure 4 Simplifed diagram o RNA

107
2 M O L E C U L AR B I O LO G Y

covalent bond
P P
chain on the upper let side o the pentose sugar. The positions o
S these carbon atoms are shown in fgure 1 .
A T S
To show the structure o RNA, draw a polymer o nucleotides, with a
P P line to show the covalent bond linking the phosphate group o each
S nucleotide to the pentose in the next nucleotide. The phosphate is
C G S linked to C 3 o the pentose  the carbon atom that is on the lower let.
P P I you have drawn the structure o RNA correctly, the two ends o
the polymer will be dierent. They are reerred to as the 3  and the 5 
S
T A S terminals.

P P  The phosphate o another nucleotide could be linked to the C 3


atom o the 3  terminal.
S
G C S  The pentose o another nucleotide could be linked to the
P P
phosphate o the 5  terminal.
Hydrogen bonds are formed To show the structure o DNA, draw a strand o nucleotides, as with
between two bases
RNA, then a second strand alongside the frst. The second strand
Key: should be run in the opposite direction, so that at each end o the DNA
S  sugar P  phosphate
molecule, one strand has a C 3 terminal and the other a C 5 terminal. The
A C two strands are linked by hydrogen bonds between the bases. Add letters
 nitrogenous bases
T G or names to indicate the bases. Adenine (A) only pairs with thymine (T)
and cytosine (C ) only pairs with guanine (G) .
 Figure 5 Simplifed diagram o DNA

5 end Structure of DNa


3 end
complementary
DNA is a double helix made of two antiparallel strands
S
P P base pairs of nucleotides linked by hydrogen bonding between
S T A S
P hydrogen
complementary base pairs.
S G C S bonds D rawings o the structure o D NA on paper cannot show all eatures o
P P
C G S the three-dimensional structure o the molecule. Figure 6 represents
S
P some o these eatures.
S T A S
P P  Each strand consists o a chain o nucleotides linked by covalent bonds.
S
P P  The two strands are parallel but run in opposite directions so they are
S C G S said to be antiparallel. O ne strand is oriented in the direction 5  to 3 
P and the other is oriented in the direction 3  to 5 .
S T A S
P
G C
P  The two strands are wound together to orm a double helix.
S S
P  The strands are held together by hydrogen bonds between the
S T A S nitrogenous bases. Adenine ( A) is always paired with thymine
P P sugarphosphate
S ( T) and guanine ( G) with cytosine ( C ) . This is reerred to as
backbone
P P comp lementary base p airing, meaning that A and T complement
S C G S each other by orming base pairs and similarly G and C complement
P
S G C S 3 end each other by orming base pairs.
P
5 end
 Figure 6 The double helix

108
2 . 6 s tru ctu r e o f d n a an d r n a

d-b qi: The bases in DNA


Look at the molecular models in fgure 7 and 3 Identiy three similarities between adenine
answer the ollowing questions. and guanine. [3 ]
1 S tate one dierence between adenine and 4 C ompare the structure o cytosine and
the other bases. [1 ] thymine. [4]
2 Each o the bases in D NA has a nitrogen 5 Although the bases have some shared
atom bonded to a hydrogen atom in a eatures, each one has a distinctive chemical
similar position, which appears in the lower structure and shape. Remembering the
let in each case in fgure 7. D educe how unction o D NA, explain the importance or
this nitrogen is used when a nucleotide is the bases each to be distinctive. [5 ]
being assembled rom its subunits. [2 ]

Guanine Adenine Cytosine Thymine


 Figure 7

Molecular models
Using models as representation of the real world:
Crick and Watson used model-making to discover the
structure of DNA.
The word model in English is derived rom the Latin word modus,
meaning manner or method. Models were originally architects
plans, showing how a new building might be constructed. Three-
dimensional models were then developed to give a more realistic
impression o what a proposed building would be like.
Molecular models also show a possible structure in three dimensions,
but whereas architects models are used to decide whether a building
should become reality in the uture, molecular models help us to
discover what the structure o a molecule actually is.
Models in science are not always three- dimensional and do not
always propose structures. They can be theoretical concepts and
they can represent systems or processes. The common eature o
models is that they are proposals, which are made to be tested. As
with architecture, models in science are oten rej ected and replaced.
Model- making played a critical part in C rick and Watsons discovery
o the structure o D NA, but it took two attempts beore they were
successul.

109
2 M O L E C U L AR B I O LO G Y

toK
crik nd Wtsons models of DNa struture
Wha is he relaive rle  Crick and Watsons discovery o the structure o DNA
cmpeiin and cperain in
scienifc research? using model-making.
Three prominent research groups C rick and Watsons success in discovering the structure o D NA was
openly competed to elucidate the based on using the evidence to develop possible structures or D NA
structure o DNA: Watson and Crick and testing them by model- building. Their rst model consisted o a
were working at Cambridge; Maurice triple helix, with bases on the outside o the molecule and magnesium
Wilkins and Rosalind Franklin were holding the two strands together with ionic bonds to the phosphate
working at Kings College o the groups on each strand. The helical structure and the spacing between
University o London; and Linus subunits in the helix tted the X- ray diraction pattern obtained by
Pauling's research group was operating Rosalind Franklin.
out o Caltech in the United States. It was dicult to get all parts o this model to t together satisactorily
A stereotype o scientists is that they and it was rej ected when Franklin pointed out that there would not
take a dispassionate approach to be enough magnesium available to orm the cross links between the
investigation. The truth is that science is strands. Another deciency o this rst model was that is that it did
a social endeavour involving a number not take account o C hargas nding that the amount o adenine
o emotion-infuenced interactions equals the thymine and the amount o cytosine equals the amount
between science. In addition to the o guanine.
joy o discovery, scientists seek the To investigate the relationship between the bases in D NA pieces o
esteem o their community. Within cardboard were cut out to represent their shapes. These showed that
research groups, collaboration is A- T and C - G base pairs could be ormed, with hydrogen bonds linking
important, but outside o their research the bases. The base pairs were equal in length so would t between
group competition oten restricts open two outer sugar-phosphate backbones.
communication that might accelerate
the pace o scientic discovery. On the Another fash o insight was needed to make the parts o the
other hand, competition may motivate molecule t together: the two strands in the helix had to run in
ambitious scientists to work tirelessly. opposite directions  they must be antiparallel. C rick and Watson
were then able to build their second model o the structure o
D NA. They used metal rods and sheeting cut to shape and held
together with small clamps. B ond lengths were all to scale and bond
angles correct. Figure 8 shows C rick and Watson with the newly
constructed model.
The model convinced all those who saw it. A typical comment was It
j ust looked right. The structure immediately suggested a mechanism
or copying D NA. It also led quickly to the realization that the genetic
code must consist o triplets o bases. In many ways the discovery o
D NA structure started the great molecular biology revolution, with
eects that are still reverberating in science and in society.

 Figure 8 Crick and Watson and their DNA model

110
2 . 7 d n a r e P l i c at i o n , t r a n s c r i P t i o n a n d t r a n s l at i o n

2.7 dna p, p


 
understnding applictions
 The replication o DNA is semi-conservative and  Use o Taq DNA polymerase to produce multiple
depends on complementary base pairing. copies o DNA rapidly by the polymerase chain
 Helicase unwinds the double helix and reaction (PCR) .
separates the two strands by breaking  Production o human insulin in bacteria as an
hydrogen bonds. example o the universality o the genetic code
 DNA polymerase links nucleotides together to allowing gene transer between species.
orm a new strand, using the pre-existing strand
as a template.
 Transcription is the synthesis o mRNA Skills
copied rom the DNA base sequences by RNA  Use a table o the genetic code to deduce which
polymerase. codon(s) corresponds to which amino acid.
 Translation is synthesis o polypeptides on  Analysis o Meselson and Stahls results
ribosomes. to obtain support or the theory o semi-
 The amino acid sequence o polypeptides is conservative replication o DNA.
determined by mRNA according to the genetic  Use a table o mRNA codons and their
code. corresponding amino acids to deduce the
 Codons o three bases on mRNA correspond to sequence o amino acids coded by a short
one amino acid in a polypeptide. mRNA strand o known base sequence.
 Translation depends on complementary  Deducing the DNA base sequence or the
base pairing between codons on mRNA and mRNA strand.
anticodons on tRNA.
Ntre of science
 Obtaining evidence or scientifc theories:
Meselson and Stahl obtained evidence or the
semi-conservative replication o DNA.

Semi-conservtive repliction of DNa


The replication o DNA is semi-conservative and depends
on complementary base pairing.
When a cell prepares to divide, the two strands o the double helix
separate ( see fgure 2 ) . Each o these original strands serves as a guide,
or template, or the creation o a new strand. The new strands are
ormed by adding nucleotides, one by one, and linking them together.
The result is two D NA molecules, both composed o an original strand
and a newly synthesized strand. For this reason, D NA replication is
reerred to as being semi-conservative.
111
2 M O L E C U L AR B I O LO G Y

The base sequence on the template strand determines the base sequence on
the new strand. Only a nucleotide carrying a base that is complementary to
adenine thymine
the next base on the template strand can successully be added to the new
strand (fgure 1 ) .
This is because complementary bases orm hydrogen bonds with each
other, stabilizing the structure. I a nucleotide with the wrong base started
cytosine guanine to be inserted, hydrogen bonding between bases would not occur and the
nucleotide would not be added to the chain. The rule that one base always
pairs with another is called complementary base pairing. It ensures
that the two D NA molecules that result rom DNA replication are identical
in their base sequences to the parent molecule that was replicated.
guanine cytosine

obtaining evidence fr the thery f semi-


thymine adenine
cnservative replicatin
Obtaining evidence or scientifc theories: Meselson
 Figure 1 and Stahl obtained evidence or the semi-conservative
replication o DNA.
S emi- conservative replication is an example o a scientifc theory that
Parental DNA seemed intuitively right, but nonetheless needed to be backed up
with evidence. Laboratories around the world attempted to confrm
G C
C G experimentally that replication o D NA is semi- conservative and soon
C G convincing evidence had been obtained.
A T

In 1 95 8 Matthew Meselson and Franklin S tahl published the results


G C
T A
o exceedingly elegant experiments that provided very strong
T A evidence or semi- conservative replication. They used 1 5 N, a rare
C G
Replication fork isotope o nitrogen that has one more neutron than the normal
14
A T N isotope, so is denser. In the 1 93 0s Harold Urey had developed
G C
A T methods o puriying stable isotopes that could be used as tracers in
G C C
T A T A
biochemical pathways. 1 5 N was one o these.
T A T A
C C G Meselson and S tahl devised a new method o separating D NA
C
G
containing 1 5 N in its bases rom D NA with 1 4N. The technique is
C G
A
T A called caesium chloride density gradient centriugation. A solution
A T
A T
A T o caesium chloride is spun in an ultracentriuge at nearly 45 , 000
A T
revolutions per minute or 2 0 hours. The dense caesium ions tend
G C
A T
G C to move towards the bottom o the tube but do not sediment ully
A T
T A
T A
because o diusion. A gradient is established, with the greatest
G
G C caesium concentration, and thereore density, at the bottom and
Parental New New Parental the lowest at the top o the tube. Any substance centriuged with
strand strand strand strand the caesium chloride solution becomes concentrated at a level
 Figure 2 Semi-conservative replication corresponding with its density.
Meselson and S tahl cultured the bacterium E. coli or ourteen
generations in a medium where the only nitrogen source was 1 5 N.
Almost all nitrogen atoms in the bases o the D NA in the bacteria
were thereore 1 5 N. They then transerred the bacteria abruptly to a
medium in which all the nitrogen was 1 4 N. At the temperature used
to culture them, the generation time was 5 0 minutes  the bacteria
divided and thereore replicated their D NA once every 5 0 minutes.

112
2 . 7 d n a r e P l i c at i o n , t r a n s c r i P t i o n a n d t r a n s l at i o n

Meselson and S tahl collected samples o D NA rom the bacterial avy


culture or several hours rom the time when it was transerred to nw xpm hqu
the 1 4 N medium. They extracted the D NA and measured its density
by caesium chloride density gradient centriugation. The D NA Meselson and Stahl used three
could be detected because it absorbs ultraviolet light, and so techniques in their experiments
created a dark band when the tubes were illuminated with that that were relatively new.
ultraviolet. Figure 3 shows the results. In the next part o this Identiy a technique used by
sub- topic there is guidance in how to analyse the changes in them that was developed:
position o the dark bands. a) by Urey in the 1930s
b) by Pickels in the 1 940s
c) by M eselson and Stahl
them selves in the 1 950s.

avy
0 0.3 0.7 1.0 1.5 2.0 2.5 3.0 4.0
Mg h vy
generations
To model helicase activity you
 Figure 3
could use some two-stranded rope
or string and a split key ring. The
strands in the rope are helical and
represent the two strands in DNA.
Meselson nd Sthls DNa repliction Open the key ring and put one
strand o the rope inside it. Close
experiments the ring so that the other strand
Analysis o Meselson and Stahls results to obtain support is outside. Slide the ring along the
string to separate the strands.
or the theory o semi-conservative replication o DNA. What problems are revealed by this
The data- based question below will guide you through the analysis o model o the activity o helicase?
Meselson and S tahls results and help to build your skills in this aspect Use the internet to fnd the solution
o science. used by living organisms.

d-b qu: The Meselson and Stahl experiment


In order or cell division to occur, DNA must be to a 1 4N medium. S amples o the bacteria were
duplicated to ensure that progeny cells have the taken over a period o time and separated by
same genetic inormation as the parent cells. The density gradient centriugation, a method in
process o duplicating DNA is termed replication. which heavier molecules settle urther down
The MeselsonStahl experiment sought to in acentriuge tube than lighter ones.
understand the mechanism o replication. Did it
1 The single band o D NA at the start
occur in a conservative ashion, a semi-conservative
( 0 generations) had a density o 1 . 72 4 g cm -3 .
ashion or in a dispersive ashion (see fgure 4) ?
The main band o D NA ater our generations
Meselson and Stahl grew E. coli in a medium had a density o 1 . 71 0 g cm -3 . Explain how
containing heavy nitrogen ( 1 5 N) or a number D NA with a lower density had been produced
o generations. They then transerred the bacteria by the bacteria. [2 ]

113
2 M O L E C U L AR B I O LO G Y

2 a) Estimate the density o the D NA ater one 6 Predict the results o centriuging a
generation. [2 ] mixture o D NA rom 0 generations and
2  generations. [2 ]
b) Explain whether the density o D NA ater
one generation alsifes any o the three
possible mechanisms or D NA replication
shown in fgure 4. [3 ]
3 a) D escribe the results ater two generations,
including the density o the D NA. [3 ]
b) E xplain whether the results ater
two generations alsiy any o the
three possible mechanisms or D NA
replication. [3 ]
4 Explain the results ater three and our
generations. [2 ]
5 Figure 4 shows D NA rom E. coli at the start
( 0 generations) and ater one generation,
with strands o D NA containing 1 5 N shown
red and strands containing 1 4N shown green.
Redraw either ( a) , ( b) or ( c) , choosing the
mechanism that is supported by Meselson
and S tahls experiment. Each D NA molecule Dispersive Conservative Semi-conservative
can be shown as two parallel lines rather Newly synthesized strand
than a helix and the colours do not have to Original template strand
be red and green. D raw the D NA or two  Figure 4 Three possible mechanisms for
more generations o replication in a medium DNA replication
containing 1 4N. [3 ]

Helicase
Helicase unwinds the double helix and separates the two
strands by breaking hydrogen bonds.
B eore D NA replication can occur, the two strands o the molecule
must separate so that they can each act as a template or the ormation
o a new strand. The separation is carried out by helicases, a group o
enzymes that use energy rom ATP. The energy is required or breaking
hydrogen bonds between complementary bases.
One well-studied helicase consists o six globular polypeptides arranged
in a donut shape. The polypeptides assemble with one strand o the D NA
molecule passing through the centre o the donut and the other outside
it. Energy rom ATP is used to move the helicase along the DNA molecule,
breaking the hydrogen bonds between bases and parting the two stands.
D ouble- stranded D NA cannot be split into two strands while it is still
helical. Helicase thereore causes the unwinding o the helix at the same
time as it separates the strands.

114
2 . 7 d n a r e P l i c at i o n , t r a n s c r i P t i o n a n d t r a n s l at i o n

DNa polymese
DNA polymerase links nucleotides together to form a new
strand, using the pre-existing strand as a template.
O nce helicase has unwound the double helix and split the D NA into two
strands, replication can begin. Each o the two strands acts as a template
or the ormation o a new strand. The assembly o the new strands is
carried out by the enzyme D NA polymerase.
D NA polymerase always moves along the template strand in the same
direction, adding one nucleotide at a time. Free nucleotides with each
o the our possible bases are available in the area where D NA is being
replicated. Each time a nucleotide is added to the new strand, only
one o the our types o nucleotide has the base that can pair with the
base at the position reached on the template strand. D NA polymerase
brings nucleotides into the position where hydrogen bonds could orm,
but unless this happens and a complementary base pair is ormed, the
nucleotide breaks away again.
O nce a nucleotide with the correct base has been brought into position
and hydrogen bonds have been ormed between the two bases, D NA
polymerase links it to the end o the new strand. This is done by
making a covalent bond between the phosphate group o the ree
nucleotide and the sugar o the nucleotide at the existing end o the
new strand. The pentose sugar is the 3  terminal and the phosphate
group is the 5  terminal, so D NA polymerase adds on the 5  terminal o
the ree nucleotide to the 3  terminal o the existing strand.
D NA polymerase gradually moves along the template strand, assembling
the new strand with a base sequence complementary to the template
strand. It does this with a very high degree o fdelity  very ew mistakes
are made during D NA replication.

Pcr  the polymese hin etion


Use of Taq DNA polymerase to produce multiple copies of DNA rapidly by the
polymerase chain reaction (PCR) .
The polymerase chain reaction ( PC R) is a o them so they hold the two strands together
technique used to make many copies o a selected successully at the temperatures normally
D NA sequence. O nly a very small quantity o the encountered by most cells. I D NA is heated to a
D NA is needed at the start. The D NA is loaded high temperature, the hydrogen bonds eventually
into a PC R machine in which a cycle o steps break and the two strands separate. I the D NA
repeatedly doubles the quantity o the selected is then cooled hydrogen bonds can orm, so the
D NA. This involves double- stranded D NA being strands pair up again. This is called re- annealing.
separated into two single strands at one stage o
The PC R machine separates DNA strands by heating
the cycle and single strands combining to orm
them to 95 C or fteen seconds. It then cools
double-stranded D NA at another stage.
the DNA quickly to 5 4 C . This would allow re-
The two strands in D NA are held together by annealing o parent strands to orm double-stranded
hydrogen bonds. These are weak interactions, DNA. However, a large excess o short sections o
but in a D NA molecule there are large numbers single-stranded DNA called primers is present. The

115
2 M O L E C U L AR B I O LO G Y

primers bind rapidly to target sequences and as a strands. It would work at the lower temperature
large excess o primers is present, they prevent the o 5 4 C that is used to attach the primers, but
re-annealing o the parent strands. C opying o the its optimum temperature is 72 C . The reaction
single parent strands then starts rom the primers. mixture is thereore heated to this temperature or
the period when Taq DNA polymerase is working.
The next stage in PCR is synthesis o double-
At this temperature it adds about 1 ,000 nucleotides
stranded DNA, using the single strands with
per minute, a very rapid rate o DNA replication.
primers as templates. The enzyme Taq DNA
polymerase is used to do this. It was obtained rom When enough time has elapsed or replication
a bacterium, Thermus aquaticus, ound in hot springs, o the selected base sequence to be complete,
including those o Yellowstone National Park. The the next cycle is started by heating to 95 C . A
temperatures o these springs range rom 50 C to cycle o PC R can be completed in less than two
80 C. Enzymes in most organisms would rapidly minutes. Thirty cycles, which ampliy the D NA
denature at such high temperatures, but those o by a actor o a billion, take less than an hour.
Thermus aquaticus, including its DNA polymerase, are With the help o Taq D NA polymerase, PC R allows
adapted to be very heat-stable to resist denaturation. the production o huge numbers o copies o a
selected base sequence in a very short time.
Taq DNA polymerase is used because it can resist
the brie period at 95 C used to separate the DNA

Select the DNA


sequence to be copied

Twice as many DNA Raise temperature


molecules can be copied 15 seconds to 95C to separate
in the next cycle the two strands

Lower temperature
80 seconds abruptly to 54C to
25 seconds
Raise temperature to 72C to allow binding of
allow rapid DNA replication by primers to DNA
Taq DNA polymerase
 Figure 5  Figure 6

Transcription
Transcription is the synthesis of mRNA copied from the
DNA base sequences by RNA polymerase.
This sequence o bases in a gene does not, in itsel, give any observable
characteristic in an organism. The unction o most genes is to speciy the
sequence o amino acids in a particular polypeptide. It is proteins that
oten directly or indirectly determine the observable characteristics o an
individual. Two processes are needed to produce a specifc polypeptide,
using the base sequence o a gene. The frst o these is transcrip tion.
Transcription is the synthesis o RNA, using D NA as a template. B ecause
RNA is single- stranded, transcription only occurs along one o the two
strands o D NA. What ollows is an outline o transcription:
 The enzyme RNA polymerase binds to a site on the D NA at the start
o a gene.
116
2 . 7 d n a r e P l i c at i o n , t r a n s c r i P t i o n a n d t r a n s l at i o n

 RNA polymerase moves along the gene separating D NA into single


strands and pairing up RNA nucleotides with complementary bases
on one strand o the D NA. There is no thymine in RNA, so uracil
pairs in a complementary ashion with adenine.
 RNA polymerase orms covalent bonds between the RNA nucleotides.
 The RNA separates rom the D NA and the double helix reorms.
 Transcription stops at the end o the gene and the completed RNA
molecule is released.
The product o transcription is a molecule o RNA with a base sequence
that is complementary to the template strand o D NA. This RNA has a
base sequence that is identical to the other strand, with one exception 
there is uracil in place o thymine. So, to make an RNA copy o the
base sequence o one strand o a D NA molecule, the other strand is
transcribed. The D NA strand with the same base sequence as the RNA
is called the sense strand. The other strand that acts as the template
and has a complementary base sequence to both the RNA and the sense
strand is called the antisense strand.

RNA polymerase
free RNA nucleotides

direction of antisense strand of DNA


transcription

3
5
3 5

RNA molecule
sense strand of DNA

 Figure 7

Translation DNA

Translation is synthesis of polypeptides on ribosomes.


TRANSCRIPTION

The second o the two processes needed to produce a specifc


polypeptide is translation. Translation is the synthesis o a polypeptide,
with an amino acid sequence determined by the base sequence o a
molecule o RNA. The production o RNA by transcription and how its
base sequence is determined by a gene was described in the previous RNA
part o this sub- topic.
TRANSLATION

Translation takes place on cell structures in the cytoplasm known as


ribosomes. Ribosomes are complex structures that consist o a small and
a large subunit, with binding sites or each o the molecules that take part
in the translation. Figure 9 shows the two subunits o a ribosome. Each is
composed o RNA molecules (pink and yellow) and proteins (purple) . Part
o the large subunit (green) is the site that makes peptide bonds between POLYPEPTIDE
amino acids, to link them together into a polypeptide.  Figure 8

117
2 M O L E C U L AR B I O LO G Y

 Figure 9 Large and small subunits of the ribosome with proteins shown in purple, ribosomal
RNA in pink and yellow and the site that catalyses the formation of peptide bonds green

Messenge rNa nd the genetic code


The amino acid sequence of polypeptides is determined
by mRNA according to the genetic code.
RNA that carries the inormation needed to synthesize a polypeptide
is called messenger RNA, usually abbreviated to mRNA. The length o
mRNA molecules varies depending on the number o amino acids in the
polypeptide but an average length or mammals is about 2,000 nucleotides.
In the genome there are many dierent genes that carry the inormation
needed to make a polypeptide with a specifc amino acid sequence. At
any time a cell will only need to make some o these polypeptides. O nly
certain genes are thereore transcribed and only certain types o mRNA
will be available or translation in the cytoplasm. C ells that need or
secrete large amounts o a particular polypeptide make many copies o
the mRNA or that polypeptide. For example, insulin- secreting cells in
the pancreas make many copies o the mRNA needed to make insulin.
Although most RNA is mRNA, there are other types; or example,
transer RNA is involved in decoding the base sequence o mRNA into an
amino acid sequence during translation and ribosomal RNA is part o the
structure o the ribosome. They are usually reerred to as tRNA and rRNA.

data-base questions: Interpreting electron micrographs


The electron micrographs in fgure 1 0 show show up more clearly. Identiy each o these
transcription, translation and D NA replication. structures:
1 D educe, with reasons, which process is a) the red structure in the central micrograph
occurring in each electron micrograph. [5 ]
b) the thin blue molecule near the lower
2 The colour in the electron micrographs has edge o the right- hand micrograph
been added to make the dierent structures

118
2 . 7 d n a r e P l i c at i o n , t r a n s c r i P t i o n a n d t r a n s l at i o n

c) the blue molecules o variable length e) the green molecules in the let- hand
attached to this thin blue molecule micrograph. [5]
d) the red molecule in the let-hand micrograph

 Figure 10

codons
Codons of three bases on mRNA correspond
to one amino acid in a polypeptide.
The translation dictionary that enables the
f s p th
cellular machinery to convert the base sequence on
p p
the mRNA into an amino acid sequence is called
the genetic code. There are our dierent bases and (5 ) u c a G (3 )
twenty amino acids, so one base cannot code or U Phe Ser Tyr Cys U
one amino acid. There are sixteen combinations o Phe Ser Tyr Cys C
two bases, which is still too ew to code or all o
Leu Ser Stop Stop A
the twenty amino acids. Living organisms thereore
use a triplet code, with groups o three bases coding Leu Ser Stop Trp G
or an amino acid. C Leu Pro His Arg U
A sequence o three bases on the mRNA is called Leu Pro His Arg C
a codon. E ach codon codes or a specifc amino Leu Pro Gln Arg A
acid to be added to the polypeptide. Table 1 lists Leu Pro Gln Arg G
all o the 64 possible codons. The three bases o an A IIe Thr Asn Ser U
mRNA codon are designated in the table as frst,
IIe Thr Asn Ser C
second and third positions.
IIe Thr Lys Arg A
Note that dierent codons can code or the same
amino acid. For example the codons GUU and
Met Thr Lys Arg G
GUC both code or the amino acid valine. For this G Val Ala Asp Gly U
reason, the code is said to be degenerate. Note Val Ala Asp Gly C
also that three codons are stop codons that code Val Ala Glu Gly A
or the end o translation.
Val Ala Glu Gly G
Amino acids are carried on another kind o RNA,
 Table 1
called tRNA. Each amino acid is carried by a
specifc tRNA, which has a three- base anticodon
complementary to the mRNA codon or that
particular amino acid.

119
2 M O L E C U L AR B I O LO G Y

Deoding base sequenes


Use of a table of the genetic code to deduce which codon(s) corresponds to which
amino acid; use of a table of mRNA codons and their corresponding amino acids to
deduce the sequence of amino acids coded by a short mRNA strand of known base
sequence; deducing the DNA base sequence for the mRNA strand.
There is no need to try to memorize the genetic base sequence complementary to the mRNA. For
code, but i a table showing it is available, you example, the codon AUG in mRNA is transcribed
should be able to make various deductions. rom the base sequence TAC on the antisense
strand o the D NA. A longer example is that
1 Which codons correspond to an amino acid?
the base sequence GUAC GUAC G is transcribed
Three letters are used to indicate each amino acid in rom C ATGC ATGC . Note that adenine pairs with
the table o the genetic code. Each o the 20 amino thymine in D NA but with uracil in RNA.
acids has between one and six codons. Read o the
three letters o each codon or the amino acid. For
Questions
example, the amino acid methionine, shown as 1 D educe the codons or
Met on the table, has one codon which is AUG. a) Tryptophan ( Trp)
2 What amino acid sequence would be b) Tyrosine ( Tyr)
translated from a sequence of codons in a
strand of mRNA? c) Arginine ( Arg) [3 ]

The frst three bases in the mRNA sequence are the 2 D educe the amino acid sequences that
codon or the frst amino acid, the next three bases correspond to these mRNA sequences: [3 ]
are the codon or the second base and so on. Look a) AC G b) C AC GGG c) C GC GC GAGG [3 ]
down the let hand side o the table to fnd the frst
3 I mRNA contains the base sequence
base o a codon, across the top o the table to fnd the
C UC AUC GAAUAAC C C
second base and down the right hand side to fnd the
third base. For example, GCA codes or the amino a) deduce the amino acid sequence o
acid alanine, which is abbreviated to Ala in the table. the polypeptide translated rom the
mRNA [2 ]
3 What base sequence in D NA would be
transcribed to give the base sequence of a b) deduce the base sequence o the
strand of mRNA? antisense strand transcribed to produce
the mRNA. [2 ]
A strand o mRNA is produced by transcribing the
anti- sense strand o the D NA. This thereore has a

codons and antiodons


Translation depends on complementary base pairing
between codons on mRNA and anticodons on tRNA.
Three components work together to synthesize polypeptides by translation:
 mRNA has a sequence o codons that specifes the amino acid
sequence o the polypeptide;
 tRNA molecules have an anticodon o three bases that binds to a
complementary codon on mRNA and they carry the amino acid
corresponding to that codon;
 ribosomes act as the binding site or mRNA and tRNAs and also
catalyse the assembly o the polypeptide.

120
2 . 7 d n a r e P l i c at i o n , t r a n s c r i P t i o n a n d t r a n s l at i o n

A summary o the main events o translation ollows:


1 An mRNA binds to the small subunit o the ribosome.
2 A molecule o tRNA with an anticodon complementary to the frst
codon to be translated on the mRNA binds to the ribosome.
3 A second tRNA with an anticodon complementary to the second
codon on the mRNA then binds. A maximum o two tRNAs can be
bound at the same time.
4 The ribosome transers the amino acid carried by the frst tRNA to the
amino acid on the second tRNA, by making a new peptide bond. The
second tRNA is then carrying a chain o two amino acids  a dipeptide.
5 The ribosome moves along the mRNA so the frst tRNA is released,
the second becomes the frst.
6 Another tRNA binds with an anticodon complementary to the next
codon on the mRNA.
7 The ribosome transers the chain o amino acids carried by the frst
tRNA to the amino acid on the second tRNA, by making a new
peptide bond.
S tages 4, 5 and 6 are repeated again and again, with one amino acid
added to the chain each time the cycle is repeated. The process continues
along the mRNA until a stop codon is reached, when the completed
polypeptide is released.
The accuracy o translation depends on complementary base pairing
between the anticodon on each tRNA and the codon on mRNA.
Mistakes are very rare, so polypeptides with a sequence o hundreds o
amino acids are regularly made with every amino acid correct.
amino acid
growing polypeptide chain
large sub unit of ribosome

tRNA

tRNA
mRNA

anticodon
 Figure 11

Production of human insulin in bacteria


Production of human insulin in bacteria as an example of the universality of the
genetic code allowing gene transfer between species.
D iabetes in some individuals is due to destruction been widely used. Porcine insulin has only one
o cells in the pancreas that secrete the hormone dierence in amino acid sequence rom human
insulin. It can be treated by inj ecting insulin into insulin and bovine insulin has three dierences.
the blood. Porcine and bovine insulin, extracted S hark insulin, which has been used or treating
rom the pancreases o pigs and cattle, have both diabetics in Japan, has seventeen dierences.

121
2 M O L E C U L AR B I O LO G Y

D espite the dierences in the amino acid sequence This may seem
between animal and human insulin, they all bind obvious, but it
to the human insulin receptor and cause lowering depends on each
o blood glucose concentration. However, some tRNA with a
diabetics develop an allergy to animal insulins, particular anticodon
so it is preerable to use human insulin. In 1 982 having the same
human insulin became commercially available or amino acid attached
the rst time. It was produced using genetically to it as in humans. In
modied E. coli bacteria. S ince then methods o other words, E. coli,
production have been developed using yeast cells yeast and safower
and more recently safower plants. ( a prokaryote, a
ungus and a plant)
Each o these species has been genetically
all use the same
modied by transerring the gene or making
genetic code as
human insulin to it. This is done in such a way
humans ( an animal) .
that the gene is transcribed to produce mRNA and
It is ortunate or  Figure 12
the mRNA is translated to produce harvestable
genetic engineers
quantities o insulin. The insulin produced has
that all organisms, with very ew exceptions, use
exactly the same amino acid sequence as i the
the same genetic code as it makes gene transer
gene was being transcribed and translated in
possible between widely diering species.
human cells.

2.8 cell respiration


 Figure 12 Text to be added.
understnding applictions
 Cell respiration is the controlled release o  Use o anaerobic cell respiration in yeasts to
energy rom organic compounds to produce produce ethanol and carbon dioxide in baking.
ATP.
 Lactate production in humans when anaerobic
 ATP rom cell respiration is immediately
respiration is used to maximize the power o
available as a source o energy in the cell. muscle contractions.
 Anaerobic cell respiration gives a small yield o
ATP rom glucose.
 Aerobic cell respiration requires oxygen and
gives a large yield o ATP rom glucose.

Ntre of science Skills


 Assessing the ethics o scientifc research:  Analysis o results rom experiments involving
the use o invertebrates in respirometer measurement o respiration rates in germinating
experiments has ethical implications. seeds or invertebrates using a respirometer.

122
2 . 8 c e l l r e s P i r at i o n

relese of enegy by cell espition


Cell respiration is the controlled release of energy from
organic compounds to produce ATP.
C ell respiration is one o the unctions o lie that all living cells perorm.
O rganic compounds are broken down to release energy, which can then
be used in the cell. For example, energy is released in muscle fbres by
breaking down glucose into carbon dioxide and water. The energy can
then be used or muscle contraction.
In humans the source o the organic compounds broken down in cell
respiration is the ood that we eat. C arbohydrates and lipids are oten
 Figure 1 Breaking down 8 grams of glucose
used, but amino acids rom proteins may be used i we eat more protein
in cell respiration provides enough energy to
than needed. Plants use carbohydrates or lipids previously made by
sprint 100 metres
photosynthesis.
C ell respiration is carried out using enzymes in a careul and controlled
way, so that as much as possible o the energy released is retained
in a usable orm. This orm is a chemical substance called adenosine
triphosphate, almost always abbreviated to ATP. To make ATP, a
phosphate group is linked to adenosine diphosphate, or AD P. E nergy
is required to carry out this reaction. The energy comes rom the
breakdown o organic compounds.
ATP is not transerred rom cell to cell and all cells require a continuous
supply. This is the reason or cell respiration being an essential unction
o lie in all cells.

aTP is  souce of enegy


cell respiration
ATP from cell respiration is immediately available as a
source of energy in the cell. ADP 1
ATP
C ells require energy or three main types o activity. phosphate

 S ynthesizing large molecules like D NA, RNA and proteins.


active cell processes
 Pumping molecules or ions across membranes by active transport.
 Figure 2
 Moving things around inside the cell, such as chromosomes,
vesicles, or in muscle cells the protein fbres that cause muscle
contraction.
The energy or all o these processes is supplied by ATP. The
advantage o ATP as an energy supply is that the energy is
immediately available. It is released simply by splitting ATP into AD P
and phosphate. The AD P and phosphate can then be reconverted to
ATP by cell respiration.
 Figure 3 Infra red photo of toucan
When energy rom ATP is used in cells, it is ultimately all converted showing that it is warmer than its
to heat. Although heat energy may be useul to keep an organism surroundings due to heat generated
warm, it cannot be reused or cell activities and is eventually lost to the by respiration. Excess heat is
environment. This is the reason or cells requiring a continual source o dissipated by sending warm blood
ATP or cell activities. to the beak

123
2 M O L E C U L AR B I O LO G Y

anerobic respirtion
Anaerobic cell respiration gives a small yield of
ATP from glucose.
Glucose is broken down in anaerobic cell respiration without using any
oxygen. The yield o ATP is relatively small, but the ATP can be produced
quickly. Anaerobic cell respiration is thereore useul in three situations:
 when a short but rapid burst o ATP production is needed;
 when oxygen supplies run out in respiring cells;
 in environments that are decient in oxygen, or example
waterlogged soils.

 Figure 4 The mud in mangrove swamps is The products o anaerobic respiration are not the same in all organisms.
defcient in oxygen. Mangrove trees have In humans, glucose is converted to lactic acid, which is usually in a
evolved vertical roots called pneumatophores dissolved orm known as lactate. In yeast and plants glucose is converted
which they use to obtain oxygen rom the air to ethanol and carbon dioxide. B oth lactate and ethanol are toxic in
excess, so must be removed rom the cells that produce them, or be
produced in strictly limited quantities.

activity S ummary equations


does bioethnol solve or mke more glucose lactate
problems? AD P ATP
There has been much debate about
This occurs in animals including humans.
bioethanol production. A renewable
fuel that cuts down on carbon
emissions is obviously desirable. glucose ethanol + carbon dioxide
What are the arguments against AD P ATP
bioethanol production?
This occurs in yeasts and plants.

Yest nd its uses


Use of anaerobic cell respiration in yeasts to produce
ethanol and carbon dioxide in baking.
Yeast is a unicellular ungus that occurs naturally in habitats where
glucose or other sugars are available, such as the surace o ruits.
It can respire either aerobically or anaerobically. Anaerobic cell
respiration in yeast is the basis or production o oods, drinks and
renewable energy.
B read is made by adding water to four, kneading the mixture to make
dough and then baking it. Usually an ingredient is added to the dough
to create bubbles o gas, so that the baked bread has a lighter texture.
Yeast is oten this ingredient. Ater kneading, the dough is kept
warm to encourage the yeast to respire. Any oxygen in the dough is
soon used up so the yeast carries out anaerobic cell respiration. The
carbon dioxide produced by anaerobic cell respiration cannot escape
rom the dough and orms bubbles. The swelling o the dough due to

 Figure 5

124
2 . 8 c e l l r e s P i r at i o n

the production o bubbles o carbon dioxide is called rising. Ethanol


is also produced by anaerobic cell respiration, but it evaporates
during baking.
B ioethanol is ethanol produced by living organisms, or use as
a renewable energy source. Although any plant matter can be
utilized as a eed stock and various living organisms can be used
to convert the plant matter into ethanol, most bioethanol is
produced rom sugar cane and corn ( maize) , using yeast. Yeast
converts sugars into ethanol in large ermenters by anaerobic
respiration. O nly sugars can be converted, so starch and cellulose
must rst be broken down into sugars. This is done using enzymes.
The ethanol produced by the yeasts is puried by distillation
and various methods are then used to remove water rom it to
improve its combustion. Most bioethanol is used as a uel in
vehicles, sometimes in a pure state and sometimes mixed with
gasoline ( petrol) .
 Figure 6

d-b qu: Monitoring anaerobic cell respiration in yeast


The apparatus in gure 7 was used to monitor 2 E xplain the loss o mass. [3 ]
mass changes during the brewing o wine. The
3 S uggest two reasons or the increasing rate
fask was placed on an electronic balance, which
o mass loss rom the start o the experiment
was connected to a computer or data-logging. The
until day 6. [2 ]
results are shown in gure 8.
4 S uggest two reasons or the mass remaining
1 C alculate the total loss o mass during the
constant rom day 1 1 onwards. [2 ]
experiment and the mean daily loss. [3 ]

airlock to
prevent 560
entry electronic
of oxygen balance
connected 555
to a data-
mass / g

logging
yeast in a computer 550
solution of
sugar and
nutrients 545

555.00 0 1 2 3 4 5 6 7 8 9 10 11 12 13
time / days
 Figure 7 Yeast data-logging apparatus  Figure 8 Monitoring anaerobic cell respiration in yeast

anerobic respirtion in humns


Lactate production in humans when anaerobic respiration is used to maximize the
power of muscle contractions.
The lungs and blood system supply oxygen to resort to anaerobic cell respiration in muscles. The
most organs o the body rapidly enough or reason is that anaerobic respiration can supply
aerobic respiration to be used, but sometimes we ATP very rapidly or a short period o time. It is

125
2 M O L E C U L AR B I O LO G Y

thereore used when we need to maximize the Ater vigorous muscle contractions, the lactate
power o muscle contractions. must be broken down. This involves the use o
oxygen. It can take several minutes or enough
In our ancestors maximally powerul muscle
oxygen to be absorbed or all lactate to be broken
contractions will have been needed or survival
down. The demand or oxygen that builds up
by allowing escape rom a predator or catching o
during a period o anaerobic respiration is called
prey during times o ood shortage. These events
the oxygen debt.
rarely occur in our lives today. Instead anaerobic
respiration is more likely to be used during
training or sport. These are examples:
 weight liters during the lit;
 short- distance runners in races up to 400
metres;
 long- distance runners, cyclists and rowers
during a sprint fnish.
Anaerobic cell respiration involves the production
o lactate, so when it is being used to supply ATP,
the concentration o lactate in a muscle increases.
There is a limit to the concentration that the body
can tolerate and this limits how much anaerobic
respiration can be done. This is the reason or the
short timescale over which the power o muscle
contractions can be maximized. We can only sprint  Figure 9 Short bursts of intense exercise are fuelled
or a short distance  not more than 400 metres. by ATP from anaerobic cell respiration

aerobic respirtion
Aerobic cell respiration requires oxygen and gives a large
yield of ATP from glucose.
I oxygen is available to a cell, glucose can be more ully broken down
to release a greater quantity o energy than in anaerobic cell respiration.
Whereas the yield o ATP is only two molecules per glucose with
anaerobic cell respiration, it is more than thirty per glucose with aerobic
cell respiration.
Aerobic cell respiration involves a series o chemical reactions. C arbon
dioxide and water are produced. In most organisms carbon dioxide is a
waste product that has to be excreted, but the water is oten useul. In
humans about hal a litre is produced per day.
glucose + oxygen carbon dioxide + water
AD P to ATP

 Figure 10 The desert rat never needs to drink In eukaryotic cells most o the reactions o aerobic cell respiration,
despite only eating dry foods, because aerobic including all o the reactions that produce carbon dioxide, happen inside
cell respiration supplies its water needs the mitochondrion.

126
2 . 8 c e l l r e s P i r at i o n

respiometes
Analysis of results from experiments involving measurement of respiration rates in
germinating seeds or invertebrates using a respirometer.
A respirometer is any device that is used to in volume. I possible the temperature inside
measure respiration rate. There are many possible the respirometer should be controlled using a
designs. Most involve these parts: thermostatically controlled water bath.
 A sealed glass or plastic container in which the Respirometers can be used to perorm various
organism or tissue is placed. experiments:
 An alkali, such as potassium hydroxide, to  the respiration rate o dierent organisms
absorb carbon dioxide. could be compared;
 A capillary tube containing fuid, connected to  the eect o temperature on respiration rate
the container. could be investigated;
O ne possible design o respirometer is shown  respiration rates could be compared in active
in gure 1 1 , but it is possible to design simpler and inactive organisms.
versions that require only a syringe with a
The table below shows the results o an experiment
capillary tube attached to it.
in which the eect o temperature on respiration in
I the respirometer is working correctly and germinating pea seeds was investigated.
the organisms inside are carrying out aerobic To analyse these results you should rst check to
cell respiration, the volume o air inside the see i the repeats at each temperature are close
respirometer will reduce and the fuid in the enough or you to decide that the results are reliable.
capillary tube will move towards the container You should then calculate mean results or each
with the organisms. This is because oxygen is used temperature. The next stage is to plot a graph o the
up and carbon dioxide produced by aerobic cell mean results, with temperature on the horizontal
respiration is absorbed by the alkali. x-axis and the rate o movement o fuid on the
The position o the fuid should be recorded vertical y-axis. Range bars can be added to the
several times. I the rate o movement o the graph by plotting the lowest and highest result at
fuid is relatively even, the results are reliable. each temperature and joining them with a ruled
I the temperature inside the respirometer line. The graph will allow you to conclude what the
fuctuates, the results will not be reliable because relationship is between the temperature and the
an increase in air temperature causes an increase respiration rate o the germinating peas.

Mvm  fud  pm


tmpu (mm m - 1 )
graduated 1 cm 3 (c) 1 2d 3d
syringe dg dg dg
5 2.0 1.5 2.0
10 2.5 2.5 3.0
wire basket containing
animal tissue 15 3.5 4.0 4.0
lter paper rolled 20 5.5 5.0 6.0
to form a wick
capillary tube 25 6.5 8.0 7.5
potassium hydroxide
solution
30 11.5 11.0 9.5
 Figure 11 Diagram of a respirometer

127
2 M O L E C U L AR B I O LO G Y

data-bas qustions: Oxygen consumption in tobacco hornworms


Tobacco hornworms are the larvae o Manduca sexta. b) S uggest reasons or the dierence in the
Adults o this species are moths. Larvae emerge trends between the periods below and
rom the eggs laid by the adult emale moths. There above the critical weight. [2 ]
are a series o larval stages called instars. Each
The researchers reared some tobacco hornworms
instar grows and then changes into the next one
in air with reduced oxygen content. They ound
by shedding its exoskeleton and developing a new
that the instar larvae moulted at a lower body mass
larger one. The exoskeleton includes the tracheal
than larvae reared in normal air with 2 0% oxygen.
tubes that supply oxygen to the tissues.
3 S uggest a reason or earlier moulting in larvae
The graphs below (fgure 1 2 ) show measurements
reared in air with reduced oxygen content. [2 ]
made using a simple respirometer o the respiration
rate o 3rd, 4th and 5 th instar larvae. D etails o before critical weight after critical weight
the methods are given in the paper published by 5th instar
0.12 0.16
the biologists who carried out the research. The 0.10 0.14
reerence to the research is C allier V and Nijhout 0.08
0.12
H F (2 01 1 ) C ontrol o body size by oxygen supply 0.06
reveals size-dependent and size-independent 0.10
0.04
mechanisms o molting and metamorphosis. 0.02 0.08
PNAS;1 08:1 46641 4669. This paper is reely 1 2 3 4 5 6 7 8 9 10 11 12 13
available on the internet at http://www.pnas.org/ respiration rate (ml O 2 /min)
content/1 08/35 /1 4664.ull.pd+ html. 0.025 0.032
4th instar
0.030
Each data point on the graphs shows the body mass 0.020
0.028
and respiration rate o one larva. For each instar the 0.015 0.026
results have been divided into younger larvae with 0.024
0.010 0.022
low to intermediate body mass and older larvae 0.020
with intermediate to high body mass. The results 0.005 0.018
are plotted on separate graphs. The intermediate 0.20.30.40.50.60.70.80.9 1.0 1.1 1.2 1.3 1.4
body mass is reerred to as the critical weight. 0.007
3rd instar 0.009
1 a) Predict, using the data in the graphs, how 0.006
0.005 0.008
the respiration rate o a larva will change 0.007
0.004
as it grows rom moulting until it reaches 0.003 0.006
the critical weight. [1 ] 0.002 0.005
0.001 0.004
b) Explain the change in respiration rate that 0.003
0.000
you have described. [2 ] 4 6 6 18
0

0.0 0.0 4
6
2
4

0.1 0 .
8
0
2

0.2

0.2
0.2
0.2
0.0

0.1
0.1
0.1

2 a) D iscuss the trends in respiration rate in weight (g) weight (g)


larvae above the critical weight. [2 ]  Figure 12 Respiration rates of tobacco hornworms (after
Callier and Nijhout, 2011)

ethics of animal us in rspiromtrs


Assessing the ethics o scientifc research: the use o invertebrates in
respirometer experiments has ethical implications.
It is important or all scientists to assess the we consider the consequences such as benefts
ethics o their research. There has been intense to students who are learning science? D o we
debate about the ethics o using animals in consider intentions? For example, i the animals
experiments. When discussing ethical issues, do are harmed unintentionally does that change

128
2 . 9 Ph o to s yn th e s i s

whether the experiment was ethical or not? Are 3 C an the risk o accidents that cause pain or
there absolute principles o right and wrong: or suering to the animals be minimized during
example, can we say that animals should never the experiment? In particular, can contact
be subj ect to conditions that are outside what with the alkali be prevented?
they would encounter in their natural habitat?
4 Is the use o animals in the experiment
B eore carrying out respirometer experiments essential or is there an alternative method that
involving animals these questions should avoids using animals?
be answered to help to decide whether the
It is particularly important to consider the ethics o
experiments are ethically acceptable:
animal use in respirometer experiments because the
1 Is it acceptable to remove animals rom their International B accalaureate Organization has issued
natural habitat or use in an experiment and a directive that laboratory or eld experiments and
can they be saely returned to their habitat? investigations need to be undertaken in an ethical
way. An important aspect o this is that experiments
2 Will the animals suer pain or any other harm
should not be undertaken in schools that infict
during the experiment?
pain or harm on humans or other living animals.

2.9 P
understnding applictions
 Photosynthesis is the production o carbon
 Changes to the Earths atmosphere, oceans and
compounds in cells using light energy. rock deposition due to photosynthesis.
 Visible light has a range o wavelengths with
violet the shortest wavelength and red the
longest. Skills
 Chlorophyll absorbs red and blue light most  Design o experiments to investigate limiting
eectively and refects green light more than actors on photosynthesis.
other colours.  Separation o photosynthetic pigments by
 Oxygen is produced in photosynthesis rom chromatography.
photolysis o water.  Drawing an absorption spectrum or chlorophyll
 Energy is needed to produce carbohydrates and and an action spectrum or photosynthesis.
other carbon compounds rom carbon dioxide.
 Temperature, light intensity and carbon dioxide
concentration are possible limiting actors on
Ntre of science
the rate o photosynthesis.  Experimental design: controlling relevant
variables in photosynthesis experiments is
essential.

129
2 M O L E C U L AR B I O LO G Y

What is photosynthesis?
Photosynthesis is the production of carbon compounds in
cells using light energy.
Living organisms require complex carbon compounds to build the
structure of their cells and to carry out life processes. S ome organisms
are able to make all the carbon compounds that they need using only
light energy and simple inorganic substances such as carbon dioxide and
water. The process that does this is called photosynthesis.
Photosynthesis is an example of energy conversion, as light energy
is converted into chemical energy in carbon compounds. The carbon
compounds produced include carbohydrates, proteins and lipids.

 Figure 2 The trees in one hectare of redwood


forest in California can have a biomass of more
than 4,000 tonnes, mostly carbon compounds
produced by photosynthesis

 Figure 1 Leaves absorb carbon dioxide and light and use them in photosynthesis

Separating photosynthetic pigments by chromatography


Separation of photosynthetic pigments by chromatography. (Practical 4)
C hloroplasts contain several types of chlorophyll
and other pigments called accessory pigments.
B ecause these pigments absorb different ranges of
wavelength of light, they look a different colour to
us. Pigments can be separated by chromatography.
You may be familiar with paper chromatography
but thin layer chromatography gives better results.
This is done with a plastic strip that has been
coated with a thin layer of a porous material.
A spot containing pigments extracted from leaf
tissue is placed near one end of the strip. A
solvent is allowed to run up the strip, to separate
the different types of pigment.

1 Tear up a leaf into small pieces and put them


in a mortar.
 Figure 3 Thin layer chromatography
2 Add a small amount of sand for grinding.

130
2 . 9 Ph o to s yn th e s i s

3 Add a small volume o propanone ( acetone) .


Pgm clu f rf
4 Use the pestle to grind the lea tissue and pgm
dissolve out the pigments.
Carotene orange 0.98
5 I the propanone all evaporates, add a little more. Chlorophyll a blue green 0.59
6 When the propanone has turned dark green, Chlorophyll b yellow green 0.42
allow the sand and other solids to settle, then
pour the propanone o into a watch glass. Phaeophytin olive green 0.81
7 Use a hair drier to evaporate o all the Xanthophyll 1 yellow 0.28
propanone and water rom the cells cytoplasm. Xanthophyll 2 yellow 0.15
8 When you have just a smear o dry pigments
in the watch glass, add 34 drops o propanone
and use a paint brush to dissolve the pigments. 1 2 Mark the outside o the tube j ust below the
level o the spot on the TLC strip.
9 Use the paint brush to transer a very small
amount o the pigment solution to the 1 3 Take the strip and cork out o the
TLC strip. Your aim is to make a very small tube.
spot o pigment in the middle o the strip, 1 4 Pour running solvent into the specimen tube
1 0 millimetres rom one end. It should be very up to the level that you marked.
dark. This is achieved by repeatedly putting a
small drop onto the strip and then allowing it 1 5 Place the specimen tube on a lab bench
to dry beore adding another amount. You can where it will not be disturbed. C areully
speed up drying by blowing on the spot or by lower the TLC strip and cork into the
using the hair drier. tube, so that the tube is sealed and the
TLC strip is j ust dipping into the running
1 0 When the spot is dark enough, slide the other solvent.  The solvent must NO T touch the
end o the strip into the slot in a cork or bung pigment spot.
that fts into a tube that is wider than the TLC
strip. The slot should hold the strip frmly. 1 6 Leave the tube completely alone or about
fve minutes, to allow the solvent to run
1 1 Insert the cork and strip into a specimen tube. up through the TLC strip. You can watch
The TLC strip should extend nearly to the the pigments separate, but D O NO T TO UC H
bottom o the tube, but not quite touch. THE  TUB E .

sp clu da rf nam f 1 7 When the solvent has nearly reached the
umb mv pgm top o the strip, remove it rom the tube and
(mm) separate it rom the cork.

1 1 8 Rule two pencil lines across the strip, one at


the level reached by the solvent and one at the
2 level o the initial pigment spot.
3 1 9 D raw a circle around each o the separated
4 pigment spots and a cross in the centre o
the circle.
5
6
7
8
 Figure 4 Chromatogram of leaf pigments
Table o standard R  values

131
2 M O L E C U L AR B I O LO G Y

2 0 Using a ruler with millimetre markings, 2 1 C alculate the R  or each pigment, where R  is
measure the distance moved by the running the distance run by the pigment divided by the
solvent ( the distance between the two lines) distance run by the solvent.
and the distance moved by each pigment ( the
22 Show all your results in the table above, starting
distance between the lower line and the cross
with the pigment that had moved least ar.
in the centre o the circle) .

Waveengths of ight
Visible light has a range o wavelengths with violet the
shortest wavelength and red the longest.
Sunlight or simply light is made up o all the wavelengths o electromagnetic
radiation that our eyes can detect. It is thereore visible to us and other
wavelengths are invisible. There is a spectrum o electromagnetic radiation
rom very short to very long wavelengths. Shorter wavelengths such as
X-rays and ultraviolet radiation have high energy; longer wavelengths such
as inrared radiation and radio waves have lower energy. Visible light has
wavelengths longer than ultraviolet and shorter than inrared. The range o
wavelengths o visible light is 400 to 700 nanometres.
When droplets o water in the sky split sunlight up and a rainbow is
ormed, dierent colours o light are visible. This is because sunlight is
a mixture o dierent wavelengths, which we see as dierent colours,
including violet, blue, green and red. Violet and blue are the shorter
wavelengths and red is the longest wavelength.
The wavelengths o light that are detected by the eye are also those used
by plants in photosynthesis. A reason or this is that they are emitted by
the sun and penetrate the E arths atmosphere in larger quantities than
other wavelengths, so are particularly abundant.

1.5 blue 5 4502 500 nm


solar radiation reaching the

green 5 5252 575 nm


Earths surface/W m 2 2

red 5 6502 700 nm


 Figure 5 In a rainbow the wavelengths of 1.0
visible light are separated

0.5

0
500 1000 1500 2000 2500 3000
wavelength /nm
 Figure 6 The spectrum of electromagnetic radiation reaching the Earths surface

light absorption by chorophy


Chlorophyll absorbs red and blue light most eectively
and refects green light more than other colours.
The frst stage in photosynthesis is the absorption o sunlight. This
involves chemical substances called pigments. A white or transparent
substance does not absorb visible light. Pigments are substances that do
132
2 . 9 Ph o to s yn th e s i s

absorb light and thereore appear coloured to us. Pigments that absorb
all o the colours appear black, because they emit no light.
There are pigments that absorb some wavelengths o visible light but
not others. For example, the pigment in a gentian fower absorbs all
colours except blue. It appears blue to us, because this part o the
sunlight is refected and can pass into our eye, to be detected by cells in
the retina.
Photosynthesizing organisms use a range o pigments, but the main
photosynthetic pigment is chlorophyll. There are various orms o
chlorophyll but they all appear green to us. This is because they absorb
red and blue light very eectively, but the intermediate green light
much less eectively. Wavelengths o green light thereore are refected.  Figure 7 Gentian fowers contain the
This is the reason or the main colour in ecosystems dominated by plants pigment delphinidin, which refects blue
being green. light and absorbs all other wavelengths.

absorption nd ction spectr


Drawing an absorption spectrum for chlorophyll and an action spectrum
for photosynthesis.
An action spectrum is a graph showing the rate It is not dicult to explain why action and absorption
o photosynthesis at each wavelength o light. spectra are very similar: photosynthesis can only
An absorption spectrum is a graph showing the occur in wavelengths o light that chlorophyll or the
percentage o light absorbed at each wavelength other photosynthetic pigments can absorb.
by a pigment or a group o pigments. 100 chlorophyll a
 When drawing both action and absorption chlorophyll b
carotenoids
spectra, the horizontal x-axis should have the
% absorption

legend wavelength, with nanometres shown


as the units. The scale should extend rom 400
to 700 nanometres.
 O n an action spectrum the y-axis should be
used or a measure o the relative amount 400 500 600 700
o photosynthesis. This is oten given as a wavelength (nm)
percentage o the maximum rate, with a scale  Figure 8 Absorption spectra o plant pigments
rom 0 to 1 00% .
100
 O n an absorption spectrum the y- axis should
have the legend % absorption, with a scale
photosynthesis
(% of max rate)

rom 0 to 1 00% .
 Ideally data points or specic wavelengths
should be plotted and then a smooth
curve be drawn through them. I this is
not possible, the curve rom a published 400 500 600 700
spectrum could be copied. wavelength (nm)
 Figure 9 Action spectrum o a plant pigment

133
2 M O L E C U L AR B I O LO G Y

data-bas qustions: Growth of tomato seedlings in red, green and blue light
Tomato seeds were germinated and grown 1 Plot a graph to show the relationship between
or 3 0 days in light produced by red, orange, wavelength, lea area and height. Hint: i
green and blue light emitting diodes. Four you need two dierent scales on the y-axis
dierent colours o LE D were tested and two you can put one on the let hand side o
combinations o colours. In every treatment the graph and the other on the right hand
the tomato plants received the same intensity side. D o not attempt to plot the results or
o photons o light. The peak wavelength o combinations o LE D s. [6]
light emitted by each wavelength is shown in
2 Using your graph, deduce the relationship
the table below, together with the mean lea
between the lea area o the seedlings and
area and height o the seedlings. Plants oten
their height. [1 ]
grow tall, with weak stems and small leaves
when they are receiving insufcient light or 3 E valuate the data in the table or a grower
photosynthesis. o tomato crops in greenhouses who is
considering using LED s to provide light. [3 ]

Pak wavngt o igt mitt la ara o sings higt o sings


coours o leds
by led (nm) (m 2 ) (mm)
Red 630 5.26 192
Orange 600 4.87 172
Green 510 5.13 161
Blue 450 7.26 128
Red and Blue  5.62 99
Red, Green and Blue  5.92 85
Source: Xiaoying, Shirong, Taotao, Zhigang and Tezuka (2012) . Regulation o the growth and photosynthesis o cherry tomato
seedlings by diferent light irradiations o light emitting diodes (LED) . African Journal of Biotechnology Vol. 11(22) , pp. 6169-6177

oxygen prductin in phtsynthesis


Oxygen is produced in photosynthesis from photolysis
of water.
O ne o the essential steps in photosynthesis is the splitting o molecules
o water to release electrons needed in other stages.
H 2 O  4e  + 4H + + O 2
This reaction is called photolysis because it only happens in the light
and the word lysis means disintegration. All o the oxygen generated
in photosynthesis comes rom photolysis o water. O xygen is a waste
product and diuses away.

efts o potosyntsis on t eart


Changes to the Earths atmosphere, oceans and rock
 Figure 10 Photosynthesizing organisms seem
deposition due to photosynthesis.
insignicant in relation to the size o the Earth Prokaryotes were the frst organisms to perorm photosynthesis, starting
but over billions o years they have changed it about 3,500 million years ago. They were joined millions o years later by
signicantly algae and plants, which have been carrying out photosynthesis ever since.

134
2 . 9 Ph o to s yn th e s i s

One consequence o photosynthesis is the rise in the oxygen concentration


o the atmosphere. This began about 2,400 million years ago (mya) , rising to av
2% by volume by 2,200 mya. This is known as the Great Oxidation Event. dfr mpr
At the same time the E arth experienced its frst glaciation, presumably Pl cmp 
due to a reduction in the greenhouse eect. This could have been due mpr (%)
to the rise in oxygenation causing a decrease in the concentration o
methane in the atmosphere and photosynthesis causing a decrease in CO 2 N2 Ar O2 H 2O
carbon dioxide concentration. B oth methane and carbon dioxide are Venus 98 1 1 0 0
potent greenhouse gases.
Earth 0.04 78 1 21 0.1
The increase in oxygen concentrations in the oceans between 2 , 400 and
2 , 2 00 mya caused the oxidation o dissolved iron in the water, causing Mars 96 2.5 1.5 2.5 0.1
it to precipitate onto the sea bed. A distinctive rock ormation was
What are the main diferences
produced called the banded iron ormation, with layers o iron oxide
between the composition o the
alternating with other minerals. The reasons or the banding are not yet
Earth's atmospheres and the
ully understood. The banded iron ormations are the most important
atmosphere o the other planets.
iron ores, so it is thanks to photosynthesis in bacteria billions o years
What is the cause o these
ago that we have abundant supplies o steel today.
diferences?
The oxygen concentration o the atmosphere remained at about 2 % rom
2 , 2 00 mya until about 75 0- 63 5 mya. There was then a signifcant rise to
2 0% or more. This corresponds with the period when many groups o
multicellular organisms were evolving.

50
oxygen/% of atmosphere

40

30 av
lg 
20
1500
10
CO 2 uptake/mol h 2 1

1000
0
4.0 3.0 2.0 1.0 0
500
Millions of years ago ( 1,000)
 Figure 11
0
75 150 225 300
200
light intensity /J dm 2 2 s 2 1
Production of carbohydrates  Figure 12 The graph shows the results
Energy is needed to produce carbohydrates and other of an experiment in which the rate
of photosynthesis was found by
carbon compounds rom carbon dioxide. measuring the uptake of carbon dioxide
Plants convert carbon dioxide and water into carbohydrates by 1 What is the reason or a CO 2
photosynthesis. The simple equation below summarizes the process: uptake rate o  200 in
carbon dioxide + water  carbohydrate + oxygen darkness?
To carry out this process, energy is required. A chemical reaction that 2 What can you predict about cell
involves putting in energy is described as endothermic. Reactions respiration and photosynthesis
involving the production o oxygen are usually endothermic in living at the point where the net rate o
systems. Reactions involving combining smaller molecules to make CO 2 uptake is zero?
larger ones are also oten endothermic and molecules o carbohydrate
such as glucose are much larger than carbon dioxide or water.

135
2 M O L E C U L AR B I O LO G Y

The energy for the conversion of carbon dioxide into carbohydrate is


ativity obtained by absorbing light. This is the reason for photosynthesis only
co 2 nentrtin occurring in the light. The energy absorbed from light does not
disappear  it is converted to chemical energy in the carbohydrates.
40
increase in biomass of grass

30
limiting fators
/kg ha - 1 h - 1

20
Temperature, light intensity and carbon dioxide
10
concentration are possible limiting factors on the
0
100 200 300 400 rate of photosynthesis.
210 CO 2 /cm 3 m - 3 air
The rate of photosynthesis in a plant can be affected by three
 Figure 13 In this graph the rate of external factors:
photosynthesis was measured  temperature;
indirectly by measuring the change in
plant biomass.  light intensity;
1 The maximum carbon  carbon dioxide concentration.
dioxide concentration of the E ach of these factors can limit the rate if they are below the optimal
atmosphere is 380 cm 3 m 3 air. level. These three factors are therefore called limiting factors.
Why is the concentration often According to the concept of limiting factors, under any combination
lower near leaves? of light intensity, temperature and carbon dioxide concentration, only
2 In what weather conditions is one of the factors is actually limiting the rate of photosynthesis. This
carbon dioxide concentration is the factor that is furthest from its optimum. If the factor is changed
likely to be the limiting factor to make it closer to the optimum, the rate of photosynthesis increases,
for photosynthesis? but changing the other factors will have no effect, as they are not the
limiting factor.
O f course, as the limiting factor is moved closer to its optimum, while
keeping the other factors constant, a point will be reached where
this factor is no longer the one that is furthest from its optimum and
another factor becomes the limiting factor. For example, at night, light
intensity is presumably the limiting factor for photosynthesis. When
the sun rises and light intensity increases, temperature will usually
take over as the limiting factor. As the temperature increases during
the morning, carbon dioxide concentration might well become the
limiting factor.

controed variabes in imiting fator


experiments
Experimental design: controlling relevant variables in
photosynthesis experiments is essential.
In any experiment, it is important to control all variables other than
the independent and dependent variable that you are investigating.
The independent variable is the one that you deliberately vary in the
experiment with a range of levels that you choose. The dependent
variable is what you measure during the experiment, to see if it is
affected by the independent variable.

136
2 . 9 Ph o to s yn th e s i s

It is essential during this type o experiment to be sure that the


independent variable is the only actor that could be aecting
the dependent variable. All other variables that might aect the
independent variable must thereore be controlled.
These are questions that you need to answer when you are designing
an experiment to investigate a limiting actor on photosynthesis:
 Which limiting actor will you investigate? This will be your
independent variable.
 How will you measure the rate o photosynthesis? This will be
your dependent variable.
 How will you keep the other limiting actors at a constant and
optimal level? These will be your controlled variables.

Investigating limiting factors


Design of experiments to investigate limiting factors
on photosynthesis.
There are many possible experimental designs. A method that can be
used to investigate the eect o carbon dioxide concentration is given
below. You could either modiy this to investigate a dierent limiting
actor or you could develop an entirely dierent design.
Investigating the efect o carbon dioxide on photosynthesis
I a stem o pondweed such as Elodea, Cabomba or Myriophyllum is acv
placed upside- down in water and the end o the stem is cut, bubbles tmprur
o gas may be seen to escape. I these are collected and tested, they 100
are ound to be mostly oxygen, produced by photosynthesis. The
% of maximum rate

rate o oxygen production can be measured by counting the bubbles.


Factors that might aect the rate o photosynthesis can be varied to 50
fnd out what eect this has. In the method below carbon dioxide
concentration is varied.
0
1 Enough water to fll a large beaker is boiled and allowed to cool. 0 10 20 30 40 50
This removes carbon dioxide and other dissolved gases. temperature/C
 Figure 14 In this graph the
2 The water is poured repeatedly rom one beaker to another, to
rate of photosynthesis was
oxygenate the water. Very little carbon dioxide will dissolve. measured indirectly by
3 A stem o pondweed is placed upside-down in the water and the measuring the change in
end o its stem is cut. No bubbles are expected to emerge, as the plant biomass
water contains almost no carbon dioxide. The temperature o the 1 What was the optimum
water should be about 25 C and the water should be very brightly temperature for
illuminated. Suitable apparatus is shown in fgure 1 6. photosynthesis in this
4 Enough sodium hydrogen carbonate is added to the beaker to raise plant?
the carbon dioxide concentration by 0.01 mol dm - 3 . I bubbles 2 What was the maximum
emerge, they are counted or 3 0 seconds, repeating the counts temperature for
until two or three consistent results are obtained. photosynthesis?

137
2 M O L E C U L AR B I O LO G Y

5 Enough sodium hydrogen carbonate is added to raise the


concentration by another 0.01 mol dm 3 . B ubble counts are done
in the same way.
sodium
hydrogen 6 The procedure above is repeated again and again until further
carbonate increases in carbon dioxide do not affect the rate of bubble
production.
Questions
1 Why are the following procedures necessary?
pondweed
a) B oiling and then cooling the water before the experiment.
b) Keeping the water at 2 5 C and brightly illuminating it.
c) Repeating bubble counts until several consistent counts have
water at 25 C
been obtained.
2 What other factor could be investigated using bubble counts with
pondweed and how would you design the experiment?
light source
3 How could you make the measurement of the rate of oxygen
production more accurate?
 Figure 15 Apparatus or measuring
photosynthesis rates in diferent
concentrations o carbon dioxide

138
Question s

Questions
1 Lipase is a digestive enzyme that accelerates a) ( i) S tate the volume units that are shown
the breakdown o triglycerides in the small in the equation. [1 ]
intestine. In the laboratory, the rate o activity ( ii) S tate the mass units that are shown in
o lipase can be detected by a decline in pH. the equation. [2 ]
Explain what causes the pH to decline. [4]
b) ( i) C alculate the mass o ATP produced per
dm 3 o oxygen. [2 ]
2 Papain is a protease that can be extracted rom ( ii) C alculate the mass o ATP produced per
pineapple ruits. Figure 1 7 shows the eect race in table 1 . [4]
o temperature on the activity o papain. The c) Explain how it is possible to synthesize such
experiment was perormed using papain dissolved large masses o ATP during races. [3 ]
in water and then repeated with the same d) D uring a 1 00 m race, 80 g o ATP is needed
quantity o papain that had been immobilized by but only 0.5 dm 3 o oxygen is consumed.
attaching it to a solid surace. The results show D educe how ATP is being produced. [3 ]
the percentage o the protein in the reaction
mixture that was digested in a fxed time. lgh f Vm f xyg cmd  c
rac/m rpra drg h rac/dm 3
100 immobilized
papain 1500 36
% of protien digested

80

60 dissolved 10,000 150


papain
40 42,300 700
20
 Table 1
0
20 30 40 50 60 70 80
temperature /C
4 Figure 1 8 shows the eects o varying light
 Figure 17 intensity on the carbon dioxide absorption
by leaves, at dierent, fxed carbon dioxide
a) ( i) O utline the eects o temperature on concentrations and temperatures.
the activity o dissolved papain. [2 ] a) D educe the limiting actor or
( ii) E xplain the eects o temperature on photosynthesis at:
the activity o dissolved papain. [2 ] ( i) W ( ii) X ( iii) Y ( iv) Z. [4]
b) ( i) C ompare the eect o temperature on b) Explain why curves I and II are the same
the activity o immobilized papain with between 1 and 7 units o light intensity. [3 ]
the eect on dissolved papain. [2 ]
c) Explain the negative values or carbon
( ii) S uggest a reason or the dierence that dioxide absorption when the leaves were in
you have described. [2 ] low light intensities. [3 ]
(iii) In some parts o the human body,
enzymes are immobilized in membranes. Z IV 0.4%CO 2 at 30C
13
rate of CO 2 absorption / arbitrary units

Suggest one enzyme and a part o the 12


body where it would be useul or it to 11
10
be immobilized in a membrane. [2] 9 III 0.4%CO 2 at 20C
8
7
6 X Y
3 The equation below summarizes the results o 5
4 II 0.13%CO 2 at 30C
metabolic pathways used to produce ATP, using 3 I 0.13%CO 2 at 20C
energy rom the oxidation o glucose. 2
1 W
glucose + oxygen + (ADP + Pi)  0
-1 1 2 3 4 5 6 7
1 80 g 1 34.4 dm 3 1 8.25 kg light intensity / arbitrary units
carbon dioxide + water + ATP  Figure 18
1 34.4 dm3 1 08 g 1 8.25 kg 139
2 M O L E C U L AR B I O LO G Y

5 Figure 1 9 shows the results o an experiment a) D escribe the relationship between


in which Chlorella cells were given light o wavelength o light and oxygen yield,
wavelengths rom 660 nm ( red) up to 700 nm when there was no supplementary light. [2 ]
( ar red) . The rate o oxygen production by b) D escribe the eect o the supplementary
photosynthesis was measured and the yield light. [2 ]
o oxygen per photon o light was calculated.
c) E xplain how the error bars help in drawing
This gives a measure o the efciency
conclusions rom this experiment. [2 ]
o photosynthesis at each wavelength.
The experiment was then repeated with d) The probable maximum yield o oxygen
supplementary light with a wavelength o was 0. 1 2 5 molecules per photon o light.
65 0 nm at the same time as each o the C alculate how many photons are needed
wavelengths rom 660 to 700 nm, but with the to produce one oxygen molecule in
same overall intensity o light as in the frst photosynthesis. [2 ]
experiment. e) O xygen production by photolysis involves
with supplementary light this reaction:
without supplementary light 4H 2 O  O 2 + 2 H 2 O + 4H + + 4e -
0.15 E ach photon o light is used to excite an
yeild of oxygen molecules per photon of light

electron ( raise it to a higher energy level) .


C alculate how many times each electron
produced by photolysis must be excited
0.10
during the reactions o photosynthesis. [2 ]

0.05

0
660 680 700
wavelength (nm)
 Figure 19 Photon yield o photosynthesis in diferent light
intensities

140
3C E LGLE Bn IEOtLI CO sG Y
Iroducio
E very living organism inherits a blueprint or allowing new combinations to be ormed by the
lie rom its parents. The inheritance o genes usion o gametes. B iologists have developed
ollows patterns. C hromosomes carry genes in techniques or artifcial manipulation o D NA,
a linear sequence that is shared by members cells and organisms.
o a species. Alleles segregate during meiosis

3.1 Genes
Uderadig Applicaio
 A gene is a heritable actor that consists o
 The causes o sickle cell anemia, including a
a length o DNA and inuences a specic base substitution mutation, a change to the
characteristic. base sequence o mRNA transcribed rom it and
 A gene occupies a specic position on one type a change to the sequence o a polypeptide in
o chromosome. hemoglobin.
 The various specic orms o a gene are alleles.  Comparison o the number o genes in humans
 Alleles difer rom each other by one or a ew with other species.
bases only.
 New alleles are ormed by mutation.
 The genome is the whole o the genetic
skill
inormation o an organism.  Use o a database to determine diferences in
the base sequence o a gene in two species.
 The entire base sequence o human genes was
sequenced in the Human Genome Project.
naure of ciece
 Developments in scientic research ollow
improvements in technology: gene sequencers,
essentially lasers and optical detectors, are
used or the sequencing o genes.

141
3 G e n e ti cs

What is a gene?
A gene is a heritable actor that consists o a length o DNA
and infuences a specic characteristic.
Genetics is the branch o biology concerned with the storage o
inormation in living organisms and how this inormation can be passed
rom parents to progeny. The word genetics was used by biologists long
beore the method o inormation storage was understood. It came
rom the word genesis, meaning origins. B iologists were interested in
the origins o eatures such as baldness, blue eyes and much more.
S omething must be the cause o these eatures and be passed on to
ospring where the eatures would again develop.
Experiments in the 1 9th century showed that there were indeed actors
in living organisms that infuenced specic characteristics and that these
actors were heritable. They could be passed on to ospring by pea
plants, ruit fies and all other organisms. There was intense research
into genetics rom the early 2 0th century onwards and the word gene
was invented or the heritable actors.
O ne obvious question was the chemical composition o genes. B y the
middle o the 2 0th century there was strong evidence that genes were
made o D NA. There are relatively ew D NA molecules in a cell  j ust 46
in a typical human cell or example  yet there are thousands o genes. We
can thereore deduce that each gene consists o a much shorter length o
D NA than a chromosome and that each chromosome carries many genes.

Comparing numbers of genes


Comparison o the number o genes in humans with other species.
How many genes does it take to make a have more genes. The table shows whether this is
bacterium, a banana plant or a bat, and how true. It gives a range o predicted gene numbers.
many are needed to make a human? We They are based on evidence rom the D NA o
see ourselves as more complex in structure, these species but are not precise counts o gene
physiology and behaviour so we might expect to numbers as these are not yet known.

Group Name of species Brief description Numbers of genes


Prokaryotes Haemophilus infuenzae Pathogenic bacterium 1,700
Escherichia coli Gut bacterium 3,200
Protoctista Trichomonas vaginalis Unicellular parasite 60,000
Fungi Saccharomyces cerevisiae (Yeast) Unicellular ungus 6,000
Plants Oryza sativa (Rice) Crop grown or ood 41,000
Arabidopsis thaliana (Thale cress) Small annual weed 26,000
Populus trichocarpa (Black cottonwood) Large tree 46,000
Animals Drosophila melanogaster (Fruit fy) Larvae consume ripe ruit 14,000
Caenorhabditis elegans Small soil roundworm 19,000
Homo sapiens (Humans) Large omnivorous biped 23,000
Daphnia pulex (Water fea) Small pond crustacean 31,000

142
3 .1 GEN Es

Where are genes located?


Activity
A gene occupies a specifc position on one type Etimating the number of
o chromosome. human gene
E xperiments in which dierent varieties o plant or animals are crossed In October 1970 Scientifc
show that genes are linked in groups and each group corresponds to one American published an estimate
o the types o chromosome in a species. For example, there are our that the human genome might
groups o linked genes in ruit fies and our types o chromosome. Maize consist o as many as 10 million
has ten groups o linked genes and ten types o chromosome and in genes. How many times greater
humans the number o both is 2 3 . than the current predicted
Each gene occupies a specic position on the type o chromosome where
number is this? What reasons
it is located. This position is called the locus o the gene. Maps showing the
can you give or such a huge
sequence o genes along chromosomes in ruit fies and other organisms
overestimate in 1970?
were produced by crossing experiments, but much more detailed maps
can now be produced when the genome o a species is sequenced.
7q31.33

7q21.11
7q36.2

7q15.2
7q31.1

7q12.1
7q21.3

7q21.3
7q14.1
7q33

7q11.22
7q31.31

7q21.13
7q22.2

7q22.2
7q32.2

7q12.3

7q14.3

7q21.1
7q35

 Figure 1 Chromosome 7: an example o a human chromosome. It consists o a single DNA


molecule with approximately 170 million base pairs  about 5% o the human genome. The
pattern o banding, obtained by staining the chromosome, is diferent rom other human
chromosomes. Several thousand genes are located on chromosome 7, mostly in the light
bands, each o which has a unique identiying code. The locus o a ew o the genes on
chromosome 7 is shown

What are alleles?


The various specifc orms o a gene are alleles.
Gregor Mendel is usually regarded as the ather o genetics. He crossed
varieties o pea plants, or example tall pea plants with dwar peas and
white- fowered pea plants with purple-fowered. Mendel deduced that
the dierences between the varieties that he crossed together were due
to dierent heritable actors. We now know that these pairs o heritable
actors are alternative orms o the same gene. For example there are
two orms o the gene that infuences height, one making pea plants tall
and the other making the plants dwar.
These dierent orms are called alleles. There can be more than two
alleles o a gene. O ne o the rst examples o multiple alleles to be
discovered is in mice. A gene that infuences coat colour has three
alleles, making the mice yellow, grey and black. There are three alleles
o the gene in humans that determines AB O blood groups. In some cases
there are large numbers o dierent alleles o a gene, or example the
gene that infuences eye colour in ruit fies.
As alleles are alternative orms o the same gene, they occupy the same
position on one type o chromosome  they have the same locus. O nly
one allele can occupy the locus o the gene on a chromosome. Most
animal and plant cells have two copies o each type o chromosome, so  Figure 2 Diferent coat colours in mice

143
3 G e n e ti cs

we can expect two copies o a gene to be present. These could be two o


the same allele o the gene or two dierent alleles.

Diferences between alleles


Alleles difer rom each other by one or a ew bases only.
A gene consists o a length o D NA, with a base sequence that can be
hundreds or thousands o bases long. The dierent alleles o a gene have
slight variations in the base sequence. Usually only one or a very small
number o bases are dierent, or example adenine might be present at
a particular position in the sequence in one allele and cytosine at that
position in another allele.
Positions in a gene where more than one base may be present are called
single nucleotide polymorphisms, abbreviated to S NPs and pronounced
snips. Several snips can be present in a gene, but even then the alleles o
the gene dier by only a ew bases.

Comparing genes
Use o a database to determine diferences in the base sequence o a gene
in two species
One outcome o the Human Genome Project is  C hoose Fast A and the sequence should
that the techniques that were developed have appear. C opy the sequence and paste it into
enabled the sequencing o other genomes. This a .txt fle or notepad fle.
allows gene sequences to be compared. The results  Repeat with a number o dierent species that
o this comparison can be used to determine
you want to compare and save the fles.
evolutionary relationships. Also, the identifcation
o conserved sequences allows species to be chosen  To have the computer align the sequence or
or exploring the unction o that sequence. you, download the sotware called C lustalX
and run it.
 Go to the website called GenB ank
( http://www.ncbi. nlm.nih.gov/pubmed/)  In the File menu, choose Load S equences.
 C hoose gene rom the search menu.  S elect your fle. Your sequences should show
up in the C lustalX window.
 Enter the name o a gene plus the organism,
such as cytochrome oxidase 1 ( C O X1 ) or pan  Under the Alignment menu choose D o
( chimpanzee) . C omplete Alignment. The example below
shows the sequence alignment o 9 dierent
 Move your mouse over the section Genomic
organisms.
regions, transcripts, and products until
Nucleotide Links appears. 
Figure 3

144
3 .1 GEN Es

Data-baed quetion: COX-2, smoking and stomach cancer


C O X- 2 is a gene that codes or the enzyme 2 a) Calculate the total percentage o the patients
cyclooxygenase. The gene consists o over that were smokers and the total percentage
6 , 000 nucleotides. Three single nucleotide o controls that were smokers. [2 ]
polymorphisms have been discovered that
b) Explain the conclusion that can be drawn
are associated with gastric adenocarcinoma,
rom the dierence in the percentages. [2 ]
a cancer o the stomach. O ne o these S NPs
occurs at nucleotide 1 1 9 5 . The base at this 3 D educe, with a reason, whether G or A
nucleotide can be either adenine or guanine. A at nucleotide 1 1 95 is associated with an
large survey in C hina involved sequencing both increased risk o gastric adenocarcinoma. [2 ]
copies o the C O X- 2 gene in 3 5 7 patients who 4 D iscuss, using the data, whether the risk o
had developed gastric adenocarcinoma and in gastric adenocarcinoma is increased equally
9 85 people who did not have the disease. All o in all smokers. [2 ]
these people were asked whether they had ever
smoked cigarettes.
GG AG or AA
Table 1 shows the 3 5 7 patients with gastric
adenocarcinoma categorized according to Smokers 9.8% 43.7%
whether they were smokers or non- smokers and
Non-smokers 9.5% 40.0%
whether they had two copies o C O X-2 with G
at nucleotide 1 1 95 ( GG) or at least one copy o
 Table 1 Patients with cancer
the gene with A at this position ( AG or AA) . The
results are shown as percentages. Table 2 shows
GG AG or AA
the same categorization or the 985 people who
did not have this cancer. Smokers 9.4% 35.6%
1 Predict, using the data, which o bases G or
A is more common at nucleotide 1 1 95 in Non-smokers 12.6% 42.4%
the controls. [2 ]
 Table 2 Patients without cancer

Mutation Activity
New alleles are ormed by mutation. New allele
New alleles are ormed rom other alleles by gene mutation. Mutations are Recent research into mutation
random changes  there is no mechanism or a particular mutation being involved nding the base
carried out. The most signifcant type o mutation is a base substitution. sequence o all genes in parents
One base in the sequence o a gene is replaced by a dierent base. For and their ofspring. It showed that
example, i adenine was present at a particular point in the base sequence there was one base mutation per
it could be substituted by cytosine, guanine or thymine. 1.2  10 8 bases. Calculate how
many new alleles a child is likely
A random change to an allele that has developed by evolution over
to have as a result o mutations
perhaps millions o years is unlikely to be benefcial. Almost all
in their parents. Assume that
mutations are thereore either neutral or harmul. S ome mutations
there are 25,000 human genes
are lethal  they cause the death o the cell in which the mutation
and these genes are 2,000 bases
occurs. Mutations in body cells are eliminated when the individual dies,
long on average.
but mutations in cells that develop into gametes can be passed on to
ospring and cause genetic disease. Source: Campbell, CD, et al. (2012)
Estimating the human mutation
rate using autozygosity in a founder
population. Nature Genetics, 44:
1277-1281. doi: 10.1038/ng.2418

145
3 G e n e ti cs

TOK
sickle cell anemia
What criteria can be used to The causes o sickle cell anemia, including a base
distinguish between correlation and
cause and efect? substitution mutation, a change to the base sequence
There is a correlation between high o mRNA transcribed rom it and a change to the
requencies o the sickle-cell allele sequence o a polypeptide in hemoglobin.
in human populations and high rates
S ickle- cell anemia is the commonest genetic disease in the world.
o inection with Falciparum malaria.
It is due to a mutation o the gene that codes or the alpha- globin
Where a correlation exists, it may
polypeptide in hemoglobin. The symbol or this gene is Hb. Most
or may not be due to a causal link.
humans have the allele Hb A . I a base substitution mutation converts
Consider the inormation in fgure 4
the sixth codon o the gene rom GAG to GTG, a new allele is ormed,
to decide whether sickle-cell anemia
called Hb S. The mutation is only inherited by ospring i it occurs in a
causes inection with malaria.
cell o the ovary or testis that develops into an egg or sperm.
a) b) When the Hb S allele is transcribed, the mRNA produced has GUG as its
sixth codon instead o GAG, and when this mRNA is transcribed, the
sixth amino acid in the polypeptide is valine instead o glutamic acid. This
change causes hemoglobin molecules to stick together in tissues with low
oxygen concentrations. The bundles o hemoglobin molecules that are
ormed are rigid enough to distort the red blood cells into a sickle shape.

Key These sickle cells cause damage to tissues by becoming trapped in blood
Frequency of Hb s allele (%) capillaries, blocking them and reducing blood fow. When sickle cells
1520 1015 510 05 return to high oxygen conditions in the lung, the hemoglobin bundles
break up and the cells return to their normal shape. These changes occur
Figure 4 Map ( a) shows the requency o
time ater time, as the red blood cells circulate. Both the hemoglobin and
the sickle cell allele and map
the plasma membrane are damaged and the lie o a red blood cell can be
(b) shows malaria afected areas in
Arica and Western Asia shortened to as little as 4 days. The body cannot replace red blood cells at
a rapid enough rate and anemia thereore develops.
So, a small change to a gene can have very harmul consequences
or individuals that inherit the gene. It is not known how oten this
mutation has occurred but in some parts o the world the Hb S allele is
remarkably common. In parts o East Arica up to 5 % o newborn babies
have two copies o the allele and develop severe anemia. Another 3 5 %
have one copy so make both normal hemoglobin and the mutant orm.
These individuals only suer mild anemia.

Figure 5 Micrographs o sickle cells and normal red blood cells

146
3 .1 GEN Es

Wha is a genome?
The genome is the whole of the genetic information of
an organism.
Among biologists today the word genome means the whole o the
genetic inormation o an organism. Genetic inormation is contained in
D NA, so a living organisms genome is the entire base sequence o each
o its D NA molecules.
 In humans the genome consists o the 46 molecules that orm
the chromosomes in the nucleus plus the D NA molecule in the
mitochondrion. This is the pattern in other animals, though the
number o chromosomes is usually dierent.
 In plant species the genome is the D NA molecules o chromosomes
in the nucleus plus the D NA molecules in the mitochondrion and
the chloroplast.
 The genome o prokaryotes is much smaller and consists o the D NA
in the circular chromosome, plus any plasmids that are present.

the Human Genome Projec


The entire base sequence of human genes was
sequenced in the Human Genome Project.
The Human Genome Proj ect began in 1 990. Its aim was to fnd the
base sequence o the entire human genome. This proj ect drove rapid
improvements in base sequencing techniques, which allowed a drat
sequence to be published much sooner than expected in 2 000 and a
complete sequence in 2 003 . Activity
Ethic of genome reearch
Although knowledge o the entire base sequence has not given us an
immediate and total understanding o human genetics, it has given us Ethical questions about
what can be regarded as a rich mine o data, which will be worked by genome research are worth
researchers or many years to come. For example, it is possible to predict discussing.
which base sequences are protein- coding genes. There are approximately Is it ethical to take a DNA
2 3 , 000 o these in the human genome. O riginally, estimates or the sample from ethnic groups
number o genes were much higher. around the world and
Another discovery was that most o the genome is not transcribed. sequence it without their
O riginally called j unk D NA,  it is being increasingly recognized permission?
that within these j unk regions, there are elements that aect gene Is it ethical for a biotech
expression as well as highly repetitive sequences, called satellite D NA. company to patent the
The genome that was sequenced consists o one set o chromosomes  it base sequence of a gene to
is a human genome rather than the human genome. Work continues prevent other companies
to fnd variations in sequence between dierent individuals. The vast from using it to conduct
maj ority o base sequences are shared by all humans giving us genetic research freely?
unity, but there are also many single nucleotide polymorphisms which Who should have access to
contribute to human diversity. this genetic information?
Should employers,
S ince the publication o the human genome, the base sequence o many
insurance companies and
other species has been determined. C omparisons between these genomes
law enforcement agencies
reveal aspects o the evolutionary history o living organisms that were
know our genetic makeup?
previously unknown. Research into genomes will be a developing theme
o biology in the 2 1 st century.
147
3 G e n e ti cs

techniques used for genome sequencing


Developments in scientifc research ollow improvements in technology: gene
sequencers, essentially lasers and optical detectors, are used or the sequencing
o genes.
The idea o sequencing the entire human genome fuorescent marker is used or the copies
seemed impossibly dicult at one time but ending in each o the our bases.
improvements in technology towards the end o  The samples are mixed together and all the
the 20th century made it possible, though still very
D NA copies are separated in one lane o a gel
ambitious. These improvements continued once the
according to the number o nucleotides.
project was underway and drat sequences were
thereore completed much sooner than expected.  A laser scans along the lane to make the
Further advances are allowing the genomes o other fuorescent markers fuoresce.
species to be sequenced at an ever increasing rate.  An optical detector is used to detect the
To sequence a genome, it is rst broken up into colours o fuorescence along the lane.
small lengths o D NA. Each o these is sequenced There is a series o peaks o fuorescence,
separately. To nd the base sequence o a ragment corresponding to each number o
o D NA, single- stranded copies o it are made nucleotides
using D NA polymerase, but the process is stopped  A computer deduces the base sequence rom
beore the whole base sequence has been copied the sequence o colours o fuorescence
by putting small quantities o a non- standard detected.
nucleotide into the reaction mixture. This is done
separately with non-standard nucleotides carrying
each o the our possible D NA bases. Four samples
o D NA copy o varying length are produced, each
with one o our D NA bases at the end o each
copy. These our samples are separated according
to length by gel electrophoresis. For each number
o nucleotides in the copy there is a band in j ust
one o the our tracks in the gel, rom which the
sequence o bases in the D NA can be deduced.
The maj or advance in technology that speeded up
base sequencing by automating it is this:
 C oloured fuorescent markers are used to Figure 6 Sequencing read from the DNA of Pinor Noir variety
mark the D NA copies. A dierent colour o of grape

148
3 .2 Ch rOmOsOm Es

3.2 Coooe
Udertadig Applicatio
 Prokaryotes have one chromosome consisting
 Cairnss technique or measuring the length
o a circular DNA molecule. o DNA molecules by autoradiography.
 Some prokaryotes also have plasmids but  Comparison o genome size in T2
eukaryotes do not. phage, Escherichia coli, Drosophila
 Eukaryote chromosomes are linear melanogaster, Homo sapiens and
DNA molecules associated with histone Paris japonica.
proteins.  Comparison o diploid chromosome numbers
 In a eukaryote species there are o Homo sapiens, Pan troglodytes, Canis
diferent chromosomes that carry diferent familiaris, Oryza sativa, Parascaris equorum.
genes.  Use o karyotypes to deduce sex and diagnose
 Homologous chromosomes carry the same Down syndrome in humans.
sequence o genes but not necessarily the
same alleles o those genes.
 Diploid nuclei have pairs o homologous skill
chromosomes.  Use o online databases to identiy the locus o
 Haploid nuclei have one chromosome o a human gene and its protein product.
each pair.
 The number o chromosomes is a characteristic
eature o members o a species. nature of ciece
 A karyogram shows the chromosomes o  Developments in scientic research ollow
an organism in homologous pairs o improvements in techniques: autoradiography
decreasing length. was used to establish the length o DNA
molecules in chromosomes.
 Sex is determined by sex chromosomes and
autosomes are chromosomes that do not
determine sex.

Bacterial chromoome
Prokaryotes have one chromosome consisting
o a circular DNA molecule.
The structure of prokaryotic cells was described in sub- topic 1 . 2 . In
most prokaryotes there is one chromosome, consisting of a circular D NA
molecule containing all the genes needed for the basic life processes
of the cell. The D NA in bacteria is not associated with proteins, so is
sometimes described as naked.

149
3 G e n e ti cs

B ecause only one chromosome is present in a prokaryotic cell, there


is usually only a single copy o each gene. Two identical copies are
present briefy ater the chromosome has been replicated, but this is a
preparation or cell division. The two genetically identical chromosomes
are moved to opposite poles and the cell then splits in two.

Plasmids
Some prokaryotes also have plasmids but eukaryotes
do not.
Plasmids are small extra DNA molecules that are commonly ound in
prokaryotes but are very unusual in eukaryotes. They are usually small,
circular and naked, containing a ew genes that may be useul to the cell
but not those needed or its basic lie processes. For example, genes or
antibiotic resistance are oten located in plasmids. These genes are benecial
when an antibiotic is present in the environment but are not at other times.
Plasmids are not always replicated at the same time as the chromosome
o a prokaryotic cell or at the same rate. Hence there may be multiple
copies o plasmids in a cell and a plasmid may not be passed to both cells
ormed by cell division.
C opies o plasmids can be transerred rom one cell to another, allowing
spread through a population. It is even possible or plasmids to cross
the species barrier. This happens i a plasmid that is released when a
prokaryotic cell dies is absorbed by a cell o a dierent species. It is a
natural method o gene transer between species. Plasmids are also used
by biologists to transer genes between species articially.

Figure 1 (a) Circular DNA molecule from


a bacterium (b) Bacterium preparing
to divide trimethoprim genes to help the
resistance plasmid spread

penicillin family disinfectant resistance


resistance

streptomycin family
vancomycin resistance
resistance

Figure 2 The pLW1043 plasmid

Usig autoradiography to measure DnA molecules


Developments in scientifc research ollow improvements in techniques:
autoradiography was used to establish the length o DNA molecules in chromosomes.
Quantitative data is usually considered to be D evelopments in microscopy have allowed images
the strongest type o evidence or or against a to be produced o structures that were previously
hypothesis, but in biology it is sometimes images invisible. These sometimes conrm existing ideas
that provide the most convincing evidence. but sometimes also change our understanding.

150
3 .2 Ch rOmOsOm Es

Autoradiography was used by biologists rom chromosome was a single D NA molecule or


the 1 940s onwards to discover where specic more than one, but the images produced by
substances were located in cells or tissues. C airns answered this question. They also
John C airns used the technique in a dierent revealed replication orks in D NA or the rst
way in the 1 96 0s. He obtained images o whole time. C airnss technique was used by others
D NA molecules rom E. coli bacteria. At the to investigate the structure o eukaryote
time it was not clear whether the bacterial chromosomes.

Measurig the legth of DnA molecules


Cairnss technique for measuring the length of DNA molecules by autoradiography.
John C airns produced images o D NA molecules The images produced by C airns showed that the
rom E.coli using this technique: chromosome in E. coli is a single circular D NA
molecule with a length o 1 , 1 00 m. This is
 C ells were grown or two generations in
remarkably long given that the length o the E coli
a culture medium containing tritiated
cells is only 2 m.
thymidine. Thymidine consists o the base
thymine linked to deoxyribose and is used Autoradiography was then used by other
by E. coli to make nucleotides that it uses in researchers to produce images o eukaryotic
D NA replication. Tritiated thymidine contains chromosomes. An image o a chromosome rom
tritium, a radioactive isotope o hydrogen, so the ruit fy Drosophila melanogaster was produced
radioactively labelled D NA was produced by that was 1 2 , 00 0 m long. This corresponded
replication in the E. coli cells. with the total amount o D NA known to be in a
D. melanogaster chromosome, so or this species
 The cells were then placed onto a dialysis
at least a chromosome contains one very long
membrane and their cell walls were digested
D NA molecule. In contrast to prokaryotes, the
using the enzyme lysozyme. The cells were
molecule was linear rather than circular.
gently burst to release their D NA onto the
surace o the dialysis membrane.
 A thin lm o photographic emulsion was
applied to the surace o the membrane and
let in darkness or two months. D uring that
time some o the atoms o tritium in the D NA
decayed and emitted high energy electrons,
which react with the lm.
 At the end o the two-month period the
lm was developed and examined with a
microscope. At each point where a tritium
atom decayed there is a dark grain. These
indicate the position o the D NA. Figure 3

Eukaryote chromosomes
Eukaryote chromosomes are linear DNA molecules
associated with histone proteins.
C hromosomes in eukaryotes are composed o D NA and protein. The
D NA is a single immensely long linear D NA molecule. It is associated
with histone proteins. Histones are globular in shape and are wider

151
3 G e n e ti cs

than the D NA. There are many histone molecules in a chromosome,


with the D NA molecule wound around them. Adj acent histones in the
chromosome are separated by short stretches o the D NA molecule that
are not in contact with histones. This gives a eukaryotic chromosome the
appearance o a string o beads during interphase.

Diferences between chromosomes


In a eukaryote species there are diferent chromosomes
that carry diferent genes.
Eukaryote chromosomes are too narrow to be visible with a light
microscope during interphase. During mitosis and meiosis the
chromosomes become much shorter and atter by supercoiling, so are
Figure 4 In an electron micrograph the visible i stains that bind either D NA or proteins are used. In the frst stage
histones give a eukaryotic chromosome o mitosis the chromosomes can be seen to be double. There are two
the appearance of a string of beads during chromatids, with identical DNA molecules produced by replication.
interphase
When the chromosomes are examined during mitosis, dierent types
can be seen. They dier both in length and in the position o the
centromere where the two chromatids are held together. The centromere
can be positioned anywhere rom close to an end to the centre o the
chromosome.
OH PH There are at least two dierent types in every eukaryote but in most
phe 16S
7S DNA val species there are more than that. In humans or example there are
thr 23S
2 3 types o chromosome.
cyt b leu
PL
pro Every gene in eukaryotes occupies a specifc position on one type o
N1
glu ile chromosome, called the locus o the gene. Each chromosome type
gln f-met thereore carries a specifc sequence o genes arranged along the linear
N6
N2 D NA molecule. In many chromosomes this sequence contains over a
control loop ala
ribosomal RNA asn trp thousand genes.
N5 transfer RNAs cys
OL
leu protein coding gene tyr C rossing experiments were done in the past to discover the sequence o
ser
his ser OX1 genes on chromosome types in Drosophila melanogaster and other species.
N4 The base sequence o whole chromosomes can now be ound, allowing
asp more accurate and complete gene sequences to be deduced.
a rg OX2
N 3gly lys
Having the genes arranged in a standard sequence along a type o
OX3 ATPase
Figure 5 Gene map of the human mitochondrial chromosome allows parts o chromosomes to be swapped during meiosis.
chromosome. There are genes on both of the
two DNA strands. The chromosomes in the
nucleus are much longer, carry far more genes
Homologous chromosomes
and are linear rather than circular Homologous chromosomes carry the same sequence o
genes but not necessarily the same alleles o those genes.
I two chromosomes have the same sequence o genes they are
homologous. Homologous chromosomes are not usually identical to
each other because, or at least some o the genes on them, the alleles
are dierent.
I two eukaryotes are members o the same species, we can expect each
o the chromosomes in one o them to be homologous with at least one
chromosome in the other. This allows members o a species to interbreed.

152
3 .2 Ch rOmOsOm Es

Data-baed quetion: Comparing the chromosomes of mice Activity


and humans micocope invetigation of galic
Figure 6 shows all of the types of chromosome in mice and in coooe
humans. Numbers and colours are used to indicate sections of mouse
chromosomes that are homologous to sections of human chromosomes. 1 Garlic has large chromosomes so is an
ideal choice for looking at chromosomes.
Mouse and human genetic similarities Cells in mitosis are needed. Garlic bulbs
Mouse chromosomes Human chromosomes grow roots if they are kept for 3 or 4 days
1 2 3 4 5 6 7 8 9 1 2 3 4 5 6 7 8 9
10 8 8 7 19 11 with their bases in water, at about 25C.
6 19 19

2
9
2
3
9
7
11
8
11 Root tips with cells in mitosis are yellow
4 4 19
15
18
11
15
3
2
3
15
11
4
19 6 in colour, not white.
1 10
1 7 16 16
3
1 20
4 13
12 10
11 1 garlic bulb polystyrene
10 11 12 13 14 15 16 17 18 disc with
10 11 12 13 14 15 16 17 18
22 3 16 10
hole cut
2 5 6
6 7
2 7 7
10 22 16
18 through
10 16 14 8 3 21 5
6
22
21
5 8
22
6
19
water at 25 C beaker
19 14 21 18 18
17 5 13 12 2
12
19 20 21 22 X Y
2 Root tips are put in a mixture of a stain
19 X Y
11
Y
that binds to the chromosomes and
9

10
X acid, which loosens the connections
between the cell walls. A length of about
Figure 6 Chromosomes 5 mm is suitable. Ten parts of aceto-
orcein to one part of 1.0 mol dm -3
1 D educe the number of types of chromosomes in mice and hydrochloric acid gives good results.
in humans. [2 ]
5 mm long garlic stainacid mixture
2 Identify the two human chromosome types that are most root tip
similar to mouse chromosomes. [2 ]
watch glass
3 Identify mouse chromosomes which contain sections that are
not homologous to human chromosomes. [2 ]
3 The roots are heated in the stainacid
4 S uggest reasons for the many similarities between the mouse mixture on a hot plate, to 80C for
and human genomes. [2 ] 5 minutes. One of the root tips is put
on a microscope slide, cut in half and
5 D educe how chromosomes have mutated during the evolution
the 2.5 mm length furthest from the
of animals such as mice and humans. [2 ]
end of the root is discarded.
root tip
watch glass

Comparing the genome sizes 6


7

5
8
1

3
2
hot plate
set at
4

Comparison of genome size in T2 phage, Escherichia 80 C

coli, Drosophila melanogaster, Homo sapiens and 4 A drop of stain and a cover slip is added
and the root tip is squashed to spread
Paris japonica. out the cells to form a layer one cell
The genomes of living organisms vary by a huge amount. The smallest thick. The chromosomes can then be
genomes are those of viruses, though they are not usually regarded as examined and counted and the various
living organisms. The table on the next page gives the genome size of phases of mitosis should also be visible.
one virus and four living organisms. thumb pressing down to
O ne of the four living organisms is a prokaryote. It has much the squash root tip
smallest genome. The genome size of eukaryotes depends on the size
and number of chromosomes. It is correlated with the complexity cover microscope folded
slip slide lter paper
of the organism, but is not directly proportional. There are several
reasons for this. The proportion of the D NA that acts as functional
genes is very variable and also the amount of gene duplication varies.
153
3 G e n e ti cs

Organism Genome size Description


(million base pairs)
T2 phage 0.18 Virus that attacks
Escherichia coli
Escherichia coli 5 Gut bacterium
Drosophila melanogaster 140 Fruit fy
Homo sapiens 3,000 Humans
Paris japonica 150,000 Woodland plant

Finding the loci of human genes


Use o online databases to identiy the locus o a human gene and its
protein product.
The locus o a gene is its particular position on together with the total number o gene loci on
homologous chromosomes. Online databases can that chromosome.
be used to fnd the locus o human genes. There
is an example o such a database in the Online Gene name Description of gene
Mendelian Inheritance in Man website, maintained DRD4 A gene that codes or a dopamine
by Johns Hopkins University. receptor that is implicated in a variety o
 S earch or the abbreviation O MIM to open the neurological and psychiatric conditions.
home page. CFTR A gene that codes or a chloride channel
 C hoose Search Gene Map. protein. An allele o this gene causes
cystic brosis.
 Enter the name o a gene into the S earch
Gene Map box. This should bring up a table HBB The gene that codes or the beta-globin
with inormation about the gene, including its subunit o hemoglobin. An allele o this
locus, starting with the chromosome on which gene causes sickle cell anemia.
the gene is located. S uggestions o human F8 The gene that codes or Factor VIII, one
genes are shown on the right. o the proteins needed or the clotting o
 An alternative to entering the name o a gene blood. The classic orm o hemophilia is
is to select a chromosome rom 1 2 2 or one caused by an allele o this gene.
o the sex chromosomes X or Y. A complete TDF Testis determining actor  the gene that
sequence o gene loci will be displayed, causes a etus to develop as a male.

Haploid nuclei
Haploid nuclei have one chromosome o each pair.
A haploid nucleus has one chromosome o each type. It has one ull
set o the chromosomes that are ound in its species. Haploid nuclei in
humans contain 2 3 chromosomes or example.
Gametes are the sex cells that use together during sexual reproduction.
Gametes have haploid nuclei, so in humans both egg and sperm cells
contain 2 3 chromosomes.
154
3 .2 Ch rOmOsOm Es

Diploid nuclei
Diploid nuclei have pairs of homologous chromosomes.
A diploid nucleus has two chromosomes of each type. It has two full
sets of the chromosomes that are found in its species. D iploid nuclei in
humans contain 46 chromosomes for example.
When haploid gametes fuse together during sexual reproduction, a
zygote with a diploid nucleus is produced. When this divides by mitosis,
more cells with diploid nuclei are produced. Many animals and plants
consist entirely of diploid cells, apart from the cells that they are using to
produce gametes for sexual reproduction.
Figure 7 Mosses coat the trunks of the laurel
D iploid nuclei have two copies of every gene, apart from genes on the
trees in this forest in the Canary Islands.
sex chromosomes. An advantage of this is that the effects of harmful
Mosses are unusual because their cells are
recessive mutations can be avoided if a dominant allele is also present. haploid. In most eukaryotes the gametes are
Also, organisms are often more vigorous if they have two different alleles haploid but not the parent that produces them
of genes instead of j ust one. This is known as hybrid vigour and is the
reason for strong growth of F 1 hybrid crop plants.

Chromosome numbers
The number of chromosomes is a characteristic feature
of members of a species.
O ne of the most fundamental characteristics of a species is the number
of chromosomes. O rganisms with a different number of chromosomes
are unlikely to be able to interbreed so all the interbreeding members of
a species need to have the same number of chromosomes.
The number of chromosomes can change during the evolution of a
species. It can decrease if chromosomes become fused together or increase
if splits occur. There are also mechanisms that can cause the chromosome Figure 8 Trillium luteum cell with a diploid
number to double. However, these are rare events and chromosome number of 12 chromosomes. Two of each
numbers tend to remain unchanged over millions of years of evolution. type of chromosome are present

Comparing chromosome numbers


Comparison of diploid chromosome numbers of Homo sapiens, Pan troglodytes,
Canis familiaris, Oryza sativa, Parascaris equorum.
The Oxford English D ictionary consists of twenty eukaryotes. Some have a few large chromosomes
large volumes, each containing a large amount and others have many small ones.
of information about the origins and meanings of
All eukaryotes have at least two different types of
words. This information could have been published
chromosome, so the diploid chromosome number
in a smaller number of larger volumes or in a larger
is at least four. In some cases it is over a hundred.
number of smaller volumes. There is a parallel
The table on the next page shows the diploid
with the numbers and sizes of chromosomes in
chromosome number of selected species.

155
3 G e n e ti cs

scientifc name Englih Diploid chromoome


o pecie name number
Parascaris horse 4
equorum threadworm
Oryza sativa rice 24
Homo sapiens humans 46
Pan troglodytes chimpanzee 48
Canis amiliaris dog 78
Figure 9 Who has more chromosomes  a dog or its owner?

Data-baed quetion: Diferences in chromosome number


Plant Chromoome number Animal
Haplopappus gracilis 4 Parascaris equorum (horse threadworm)
Luzula purpurea (woodrush) 6 Aedes aegypti (yellow ever mosquito)
Crepis capillaris 8 Drosophila melanogaster (ruity)
Vicia aba (eld bean) 12 Musca domestica (house y)
Brassica oleracea (cabbage) 18 Chorthippus parallelus (grasshopper)
Citrullus vulgaris (water melon) 22 Cricetulus griseus (Chinese hamster)
Lilium regale (royal lily) 24 Schistocerca gregaria (desert locust)
Bromus texensis 28 Desmodus rotundus (vampire bat)
Camellia sinesis (Chinese tea) 30 Mustela vison (mink)
Magnolia virginiana (sweet bay) 38 Felis catus (domestic cat)
Arachis hypogaea (peanut) 40 Mus musculus (mouse)
Cofea arabica (cofee) 44 Mesocricetus auratus (golden hamster)
Stipa spartea (porcupine grass) 46 Homo sapiens (modern humans)
Chrysoplenum alterniolium (saxirage) 48 Pan troglodytes (chimpanzee)
Aster laevis (Michaelmas daisy) 54 Ovis aries (domestic sheep)
Glyceria canadensis (manna grass) 60 Capra hircus (goat)
Carya tomentosa (hickory) 64 Dasypus novemcinctus (armadillo)
Magnolia cordata 76 Ursus americanus (American black bear)
Rhododendron keysii 78 Canis amiliaris (dog)
Table 1

1 There are many different chromosome numbers 3 E xplain why the size of the genome of a
in the table, but some numbers are missing, species cannot be deduced from the number
for example, 5 , 7, 1 1 , 1 3 . Explain why none of chromosomes. [1 ]
of the species has 1 3 chromosomes. [3 ]
4 S uggest, using the data in table 1 , a change
2 D iscuss, using the data in the table, the in chromosome structure that may have
hypothesis that the more complex an occurred during human evolution. [2 ]
organism is, the more chromosomes it has. [4]

156
3 .2 Ch rOmOsOm Es

sex determination
female male
Sex is determined by sex chromosomes and autosomes XX XY
are chromosomes that do not determine sex.
There are two chromosomes in humans that determine sex:

X
X
 the X chromosome is relatively large and has its centromere near XX
the middle.

Y
X
 the Y chromosome is much smaller and has its centromere near XX XY
the end.
XY
B ecause the X and Y chromosomes determine sex they are called the sex
chromosomes. All the other chromosomes are autosomes and do not
affect whether a fetus develops as a male or female.
1 female : 1 male
The X chromosome has many genes that are essential in both males and
females. All humans must therefore have at least one X chromosome. Figure 10 Determination of gender
The Y chromosome only has a small number of genes. A small part of the
Y chromosome has the same sequence of genes as a small part of the X
chromosome, but the genes on the remainder of the Y chromosome
are not found on the X chromosome and are not needed for female
development.
O ne Y chromosome gene in particular causes a fetus to develop as a
male. This is called either S RY or TD F. It initiates the development of
male features, including testes and testosterone production. B ecause of
this gene a fetus with one X and one Y chromosome develops as a male.
A fetus that has two X chromosomes and no Y chromosome does not
have the TD F gene so ovaries develop instead of testes and female sex
hormones are produced, not testosterone.
Females have two X chromosomes. Females pass on one of their two
X chromosomes in each egg cell, so all offspring inherit an X chromosome
from their mother. The gender of a human is determined at the moment
of fertilization by one chromosome carried in the sperm. This can either
be an X or a Y chromosome. When sperm are formed, half contain the X
chromosome and half the Y chromosome. D aughters inherit their fathers
X chromosome and sons inherit his Y chromosome.

Karyogram
A karyogram shows the chromosomes of an organism
in homologous pairs of decreasing length.
The chromosomes of an organism are visible in cells that are in mitosis,
with cells in metaphase giving the clearest view. S tains have to be used
to make the chromosomes show up. S ome stains give each chromosome
type a distinctive banding pattern.
If dividing cells are stained and placed on a microscope slide and are
then burst by pressing on the cover slip, the chromosomes become
spread. O ften they overlap each other, but with careful searching a cell
can usually be found with no overlapping chromosomes. A micrograph
can be taken of the stained chromosomes.

157
3 G e n e ti cs

Originally analysis involved cutting out all the chromosomes and


TOK arranging them manually but this process can now be done digitally. The
To what extent is determining gender chromosomes are arranged according to their size and structure. The
or sporting competition a scientifc position of the centromere and the pattern of banding allow chromosomes
question? that are of a different type but similar size to be distinguished.

Gender testing was introduced at As most cells are diploid, the chromosomes are usually in homologous
the 1968 Olympic games to address pairs. They are arranged by size, starting with the longest pair and
concerns that women with ambiguous ending with the smallest.
physiological genders would have
an unair advantage. This has proven
to be problematic or a number o
reasons. The chromosomal standard
is problematic as non-disjunction can
lead to situations where an individual
might technically be male, but might
not defne hersel in that way. People
with two X chromosomes can develop
hormonally as a male and people with
an X and a Y can develop hormonally
as a emale.
The practice o gender testing was
discontinued in 1996 in part because
o human rights issues including the
right to sel-expression and the right to
identiy one's own gender. Rather than
being a scientifc question, it is more
airly a social question.

Figure 11 Karyogram o a human emale, with fuorescent staining

Karyotypes and Down syndrome


Use o karyotypes to deduce sex and diagnose Down
syndrome in humans.
A karyogram is an image of the chromosomes of an organism,
arranged in homologous pairs of decreasing length. A karyotype is a
property of an organism  it is the number and type of chromosomes
that the organism has in its nuclei. Karyotypes are studied by looking
at karyograms. They can be used in two ways:
1 To deduce whether an individual is male or female. If two XX
Figure 12 Child with trisomy 21 or chromosomes are present the individual is female whereas one X
Down syndrome and one Y indicate a male.
2 To diagnose Down syndrome and other chromosome abnormalities.
This is usually done using fetal cells taken from the uterus during
pregnancy. If there are three copies of chromosome 2 1 in the
karyotype instead of two, the child has Down syndrome. This is
sometimes called trisomy 21 . While individuals vary, some of the
component features of the syndrome are hearing loss, heart and
vision disorders. Mental and growth retardation are also common.

158
3.3 mEiOsis

Data-based questions: A human karyotype


The karyogram shows the karyotype of a fetus.
1 S tate which chromosome type is
a) longest
b) shortest. [2 ]
2 D istinguish between the structure of
a) human chromosome 2 and chromosome 1 2
b) the human X and Y chromosome. [4]
3 D educe with a reason the sex of the fetus. [2 ]
4 E xplain whether the karyotype shows any abnormalities. [2 ]

Figure 13

3.3 meo
Udertadig Applicatio
 One diploid nucleus divides by meiosis to
 Non-disjunction can cause Down syndrome
produce our haploid nuclei. and other chromosome abnormalities. Studies
 The halving o the chromosome number allows showing age o parents inuences chances o
a sexual lie cycle with usion o gametes. non-disjunction.
 DNA is replicated beore meiosis so that all  Methods used to obtain cells or karyotype
chromosomes consist o two sister chromatids. analysis e.g. chorionic villus sampling and
 The early stages o meiosis involve pairing o amniocentesis and the associated risks.
homologous chromosomes and crossing over
ollowed by condensation.
 Orientation o pairs o homologous skill
chromosomes prior to separation is random.  Drawing diagrams to show the stages o
 Separation o pairs o homologous meiosis resulting in the ormation o our
chromosomes in the rst division o meiosis haploid cells.
halves the chromosome number.
 Crossing over and random orientation promotes nature of ciece
genetic variation.
 Making careul observations: meiosis was
 Fusion o gametes rom diferent parents discovered by microscope examination o
promotes genetic variation. dividing germ-line cells.

159
3 G e n e ti cs

the discovery of meiosis


Making careful observations: meiosis was discovered by microscope examination
of dividing germ-line cells.
When improved microscopes had been developed chromosome number is doubled by ertilization. The
in the 1 9th century that gave detailed images o observation led to the hypothesis that there must be
cell structures, it was discovered that some dyes a special nuclear division in every generation that
specifcally stained the nucleus o the cell. These dyes halves the chromosome number.
revealed thread-like structures in dividing nuclei that
Nuclear divisions unlike mitosis had already
were named chromosomes. From the 1 880s onwards
been observed during gamete development in
a group o German biologists carried out careul and
both animals and plants. These divisions were
detailed observations o dividing nuclei that gradually
identifed as the method used to halve the
revealed how mitosis and meiosis occur.
chromosome number and they were named
We can appreciate the considerable achievements o meiosis. The sequence o events in meiosis was
these biologists i we try to repeat the observations eventually worked out by careul observation o
that they made. The preparation o microscope cells taken rom the ovaries o rabbits ( Oryctolagus
slides showing meiosis is challenging. Suitable tissue cuniculus) between 0 and 2 8 days old. The
can be obtained rom the developing anthers inside advantage o this species is that in emales meiosis
a lily bud or rom the testis o a dissected locust. begins at birth and occurs slowly over many days.
The tissue must be fxed, stained and then squashed
on a microscope slide. Oten no cells in meiosis are
visible or the images are not clear enough to show
details o the process. Even with prepared slides
made by experts it is difcult to understand the
images as chromosomes orm a variety o bizarre
shapes during the stages o meiosis.
A key observation was that in the horse threadworm
(Parascaris equorum) there are two chromosomes
in the nuclei o egg and sperm cells, whereas the
ertilized egg contains our. This indicated that the  Figure 1

one diploid cell


2n
Meiosis in ouline
meiosis I
One diploid nucleus divides by meiosis to produce four
haploid nuclei.
two haploid cells n n Meiosis is one o the two ways in which the nucleus o a eukaryotic
cell can divide. The other method is mitosis, which was described in
meiosis II
sub- topic 1 . 6. In meiosis the nucleus divides twice. The frst division
four haploid cells n n n n produces two nuclei, each o which divides again to give a total o our
nuclei. The two divisions are known as meiosis I and meiosis II.
Figure 2 Overview of meiosis
The nucleus that undergoes the frst division o meiosis is diploid  it
has two chromosomes o each type. C hromosomes o the same type are
known as homologous chromosomes. Each o the our nuclei produced
by meiosis has j ust one chromosome o each type  they are haploid.
Meiosis involves a halving o the chromosome number. It is thereore
known as a reduction division.
The cells produced by meiosis I have one chromosome o each type, so
the halving o the chromosome number happens in the frst division,
160
3.3 mEiOsis

not the second division. The two nuclei produced by meiosis I have the
haploid number o chromosomes, but each chromosome still consists o
two chromatids. These chromatids separate during meiosis II, producing
our nuclei that have the haploid number o chromosomes, with each
chromosome consisting o a single chromatid.

Meiosis and sexual life cycles


The halving of the chromosome number allows a sexual
life cycle with fusion of gametes.
The lie cycles o living organisms can be sexual or asexual. In an asexual
lie cycle the ospring have the same chromosomes as the parent so are
genetically identical. In a sexual lie cycle there are dierences between the
chromosomes o the ospring and the parents, so there is genetic diversity.
In eukaryotic organisms, sexual reproduction involves the process o
ertilization. Fertilization is the union o sex cells, or gametes, usually
rom two dierent parents. Fertilization doubles the number o
chromosomes each time it occurs. It would thereore cause a doubling
o chromosome number every generation, i the number was not also
halved at some stage in the lie cycle. This halving o chromosome
number happens during meiosis.
Meiosis can happen at any stage during a sexual lie cycle, but in animals
it happens during the process o creating the gametes. B ody cells are
thereore diploid and have two copies o most genes.
Meiosis is a complex process and it is not at the moment clear how it
developed. What is clear is that its evolution was a critical step in the
Figure 4 Fledgling owls (bottom) produced by
origin o eukaryotes. Without meiosis there cannot be usion o gametes a sexual life cycle have diploid body cells but
and the sexual lie cycle o eukaryotes could not occur. mosses ( top) have haploid cells

Data-baed queton: Life cycles


Figure 3 shows the lie cycle o humans and 1 O utline fve similarities between the lie
mosses, with n being used to represent the haploid cycle o a moss and o a human. [5 ]
number o chromosomes and 2 n to represent the
2 D istinguish between the lie cycles o
diploid number. Sporophytes o mosses grow on
a moss and a human by giving fve
the main moss plant and consist o a stalk and a
dierences. [5 ]
capsule in which spores are produced.
egg
n
sperm
sperm egg n
n n
moss
human male zygote human female plant zygote
2n 2n 2n n 2n

Key spore sporophyte


mitosis n 2n
meiosis
fertilization
Figure 3

161
3 G e n e ti cs

Replicatio of DnA before meiosis


DNA is replicated before meiosis so that all chromosomes
2n interphase consist of two sister chromatids.
D uring the early stages o meiosis the chromosomes gradually shorten
by supercoiling. As soon as they become visible it is clear that each
chromosome consists o two chromatids. This is because all D NA in
2n
homologous the nucleus is replicated during the interphase beore meiosis, so each
chromosomes chromosome consists o two sister chromatids.
Initially the two chromatids that make up each chromosome are
2n meiosis I
genetically identical. This is because D NA replication is very accurate and
the number o mistakes in the copying o the D NA is extremely small.
We might expect the D NA to be replicated again between the frst and
the second division o meiosis, but it does not happen. This explains how
n n meiosis II
the chromosome number is halved during meiosis. O ne diploid nucleus,
in which each chromosome consists o two chromatids, divides twice
to produce our haploid nuclei in which each chromosome consists o
n n n n one chromatid.
Figure 5 Outline of meiosis
Bivalets formatio ad crossig over
The early stages of meiosis involve pairing of homologous
chromosomes and crossing over followed by condensation.
Some o the most important events o meiosis happen at the start o meiosis
I while the chromosomes are still very elongated and cannot be seen with
a microscope. Firstly homologous chromosomes pair up with each other.
Because DNA replication has already occurred, each chromosome consists
o two chromatids and so there are our DNA molecules associated in each
pair o homologous chromosomes. A pair o homologous chromosomes is
bivalent and the pairing process is sometimes called synapsis.
Soon ater synapsis, a process called crossing over takes place. The molecular
details o this need not concern us here, but the outcome is very important.
A junction is created where one chromatid in each o the homologous
chromosomes breaks and rejoins with the other chromatid. Crossing over
occurs at random positions anywhere along the chromosomes. At least one
crossover occurs in each bivalent and there can be several.
B ecause a crossover occurs at precisely the same position on the two
chromatids involved, there is a mutual exchange o genes between the
Figure 6 A pair of homologous chromatids. As the chromatids are homologous but not identical, some
chromosomes contains four alleles o the exchanged genes are likely to be dierent. C hromatids with
chromatids and is sometimes called new combinations o alleles are thereore produced.
a tetrad. Five chiasmata are visible
in this tetrad, showing that crossing
over can occur more than once Radom orietatio of bivalets
Orientation of pairs of homologous chromosomes prior to
separation is random.
While pairs o homologous chromosomes are condensing inside the
nucleus o a cell in the early stages o meiosis, spindle microtubules are
growing rom the poles o the cell. Ater the nuclear membrane has
162
3.3 mEiOsis

broken down, these spindle microtubules attach to the centromeres o


the chromosomes.
The attachment o the spindle microtubules is not the same as in mitosis.
The principles are these:
 E ach chromosome is attached to one pole only, not to both.
 The two homologous chromosomes in a bivalent are attached to
dierent poles.
 The pole to which each chromosome is attached depends on which
way the pair o chromosomes is acing. This is called the orientation.
 The orientation o bivalents is random, so each chromosome has an equal
chance o attaching to each pole, and eventually o being pulled to it.
 The orientation o one bivalent does not aect other bivalents. The MITOSIS
consequences o the random orientation o bivalents are discussed in
the section on genetic diversity later in this topic.

Halving the chromosome number


Separation o pairs o homologous chromosomes in the
frst division o meiosis halves the chromosome number.
The movement o chromosomes is not the same in the frst division o either or
meiosis as in mitosis. Whereas in mitosis the centromere divides and the two MEIOSIS
chromatids that make up a chromosome move to opposite poles, in meiosis Figure 7 Comparison of attachment
the centromere does not divide and whole chromosomes move to the poles. of chromosomes to spindle
microtubules in mitosis and meiosis
Initially the two chromosomes in each bivalent are held together
by chiasmata, but these slide to the end o the chromosomes and
then the chromosomes can separate. This separation o homologous
chromosomes is called disj unction. O ne chromosome rom each bivalent
moves to one o the poles and the other chromosome to the other pole.
The separation o pairs o homologous chromosomes to opposite poles
o the cell halves the chromosome number o the cell. It is thereore
the frst division o meiosis that is the reduction division. B ecause one
chromosome o each type moves to each pole, both o the two nuclei
ormed in the frst division o meiosis contain one o each type o
chromosome, so they are both haploid.

Obtaining cells from a fetus


Methods used to obtain cells or karyotype analysis e.g. chorionic villus sampling
and amniocentesis and the associated risks.
Two procedures are used or obtaining cells The second procedure is chorionic villus sampling.
containing the etal chromosomes needed or A sampling tool that enters through the vagina is
producing a karyotype. Amniocentesis involves used to obtain cells rom the chorion, one o the
passing a nee dle through the mothe r' s ab domen membranes rom which the placenta develops.
wall, using ultrasound to guide the needle. This can be done earlier in the pregnancy than
The needle is used to withdraw a sample o amniocentesis, but whereas the risk o miscarriage
amniotic luid containing etal cells rom the with amniocentesis is 1 % , with chorionic villus
amniotic sac. sampling it is 2 % .

163
3 G e n e ti cs

Diagrams of the stages of meiosis


Drawing diagrams to show the stages of meiosis resulting in the formation of four
haploid cells.
In mitosis our stages are usually recognized: Usually we draw biological structures rom
prophase, metaphase, anaphase and telophase. actual specimens, oten looking at them down
Meiosis can also be divided into these stages, but a microscope. Preparation o microscope slides
each stage happens twice: in meiosis I and then a showing meiosis is worth attempting but it is
second time in meiosis II. The main events o each challenging. Permanent slides usually have more
stage in mitosis also happen in meiosis: cells visible in meiosis than temporary mounts,
but even then it is difcult to interpret the
 prophase: condensation o chromosomes;
structure o bivalents rom their appearance. This
 metaphase: attachment o spindle microtubules; is why we usually construct diagrams o meiosis
 anaphase: movement o chromosomes to rather than draw stages rom specimens on
the poles; microscope slides!

 telophase: decondensation o chromosomes.

The frst division o meiosis


Prophase i
 Cell has 2n chromosomes (double
nuclear membrane
chromatid) : n is haploid number of
chromosomes. spindle microtubules
and centriole
 Homologous chromosomes pair (synapsis) .
Prophase I
 Crossing over occurs.

metaphase i
 Spindle microtubules move homologous pairs
to equator of cell. bivalents aligned
on the equator
 Orientation of paternal and maternal
chromosomes on either side of equator
is random and independent of other Metaphase I
homologous pairs.
Anaphase i
 Homologous pairs are separated. One homologous
chromosome of each pair moves to each chromosomes
being pulled to
pole. opposite poles

Anaphase I

Telophase i
 Chromosomes uncoil. During interphase
that follows, no replication occurs. cell has divided
across the equator
 Reduction of chromosome number from
diploid to haploid completed.
Telophase I
 Cytokinesis occurs.

164
3.3 mEiOsis

The second division of meiosis


Prophae ii
 Chromosomes, which still consist of two
chromatids, condense and become visible.

Prophase II

metaphae ii

Metaphase II

Anaphae ii
 Centromeres separate and chromatids are
moved to opposite poles.

Anaphase II

Telophae ii
 Chromatids reach opposite poles.
 Nuclear envelope forms.
 Cytokinesis occurs.

Telophase II

Meiosis and genetic variation


Crossing over and random orientation promotes genetic
variation.
When two parents have a child, they know that it will inherit an
unpredictable mixture of characteristics from each of them. Much of
the unpredictability is due to meiosis. E very gamete produced by a
parent has a new combination of alleles  meiosis is a source of endless
genetic variation.
Apart from the genes on the X and Y chromosomes, humans have two
copies of each gene. In some cases the two copies are the same allele and
there will be one copy of that allele in every gamete produced by the
parent. There are likely to be thousands of genes in the parents genome
165
3 G e n e ti cs

where the two alleles are dierent. Each o the two alleles has an equal
Activity chance o being passed on in a gamete. Let us suppose that there is
I g is the number o genes a gene with the alleles A and a. Hal o the gametes produced by the
in a genome with diferent parent will contain A and hal will contain a.
alleles, 2 g is the number Let us now suppose that there is another gene with the alleles B and b.
o combinations o these Again hal o the gametes will contain B and hal b. However, meiosis
alleles that can be generated can result in gametes with dierent combinations o these genes: AB , Ab,
by meiosis. I there were aB and ab. There are two processes in meiosis that generate this diversity.
just 69 genes with diferent
alleles (3 in each o the
B
23 chromosome types in a B a
humans) there would be 50%
A b
probability
590,295,810,358,705, b
A
700,000 combinations.
B b
Assuming that all humans telophase I
are genetically diferent, and A a
that there are 7,000,000 b
50% a
humans, calculate the prophase I probability a b
percentage o all possible A B
B
genomes that currently exist. A

metaphase I
 Figure 8 Random orientation in metaphase I

1. Random orientation o bivalents


In metaphase I the orientation o bivalents is random and the orientation
o one bivalent does not infuence the orientation o any o the others.
Random orientation o bivalents is the process that generates genetic
variation among genes that are on dierent chromosome types.
For every additional bivalent, the number o possible chromosome
combinations in a cell produced by meiosis doubles. For a haploid number
o n, the number o possible combinations is 2 n. For humans with a
haploid number o 2 3 this amounts to 2 23 or over 8 million combinations.

2. Crossing over
Without crossing over in prophase I, combinations o alleles on
chromosomes would be orever linked together. For example, i one
chromosome carried the combination C D and another carried cd, only
these combinations could occur in gametes. C rossing over allows linked
genes to be reshufed, to produce new combinations such as C d and cD .
It increases the number o allele combinations that can be generated by
meiosis so much that it is eectively innite.

Fertilization and genetic variation


Fusion o gametes rom diferent parents promotes
genetic variation.
The usion o gametes to produce a zygote is a highly signicant event
both or individuals and or species.
 It is the start o the lie o a new individual.
 It allows alleles rom two dierent individuals to be combined in one
Figure 9 new individual.
166
3.3 mEiOsis

 The combination o alleles is unlikely ever to have existed beore.


 Fusion o gametes thereore promotes genetic variation in a species.
 Genetic variation is essential or evolution.

no-disjuctio ad Dow sydrome


Non-disjunction can cause Down syndrome and other chromosome abnormalities.
Meiosis is sometimes subj ect to errors. Most other trisomies in humans are so serious
O ne example o this is when homologous that the ospring do not survive. B abies are
chromosomes ail to separate at anaphase. This sometimes born with trisomy 1 8 and trisomy
is termed non- disj unction. This can happen with 1 3 . Non-disj unction can also result in the
any o the pairs o homologous chromosomes. birth o babies with abnormal numbers o sex
B oth o the chromosomes move to one pole and chromosomes. Klineelters syndrome is caused
neither to the other pole. The result will be a by having the sex chromosomes XXY. Turners
gamete that either has an extra chromosome or syndrome is caused by having only one sex
is defcient in a chromosome. I the gamete is chromosome, an X.
involved in human ertilization, the result will
be an individual with either 45 or diploid parent cell with
47 chromosomes. two chromosome 21

An abnormal number o chromosomes non-disjunction


will oten lead to a person possessing a during meiosis gamete with no
syndrome, i.e. a collection o physical chromosome 21
signs or symptoms. For example gamete with two
trisomy 2 1 , also known as D own chromosome 21
cell dies
syndrome, is due to a non- disj unction
event that leaves the individual with fusion of normal haploid

three o chromosome number 2 1 gametes gamete
instead o two. While individuals vary,
some o the component eatures o
trisomy: zygote with
the syndrome include hearing loss, three chromosome 21
heart and vision disorders. Mental and
growth retardation are also common. Figure 10 How non-disjunction can give rise to Down syndrome

trisomy 21
Paretal age ad o-disjuctio all chromosomal
abnormalities
14
Studies showing age o parents infuences chances o
incidence (% of all live births)

12
non-disjunction
The data presented in fgure 1 1 shows the relationship between 10
maternal age and the incidence o trisomy 2 1 and o other 8
chromosomal abnormalities.
6
1 O utline the relationship between maternal age and the incidence
4
o chromosomal abnormalities in live births. [2 ]
2
2 a) For mothers 40 years o age, determine the probability that
they will give birth to a child with trisomy 2 1 . [1 ] 0
20 40 60
b) Using the data in fgure 1 1 , calculate the probability that a maternal age (years)
mother o 40 years o age will give birth to a child with a  Figure 11 The incidence of trisomy 21
chromosomal abnormality other than trisomy 2 1 . [2 ] and other chromosomal abnormalities
as a function of maternal age

167
3 G e n e ti cs

3 O nly a small number of possible chromosomal abnormalities


are ever found among live births, and trisomy 2 1 is much the
commonest. S uggest reasons for these trends. [3 ]
4 D iscuss the risks parents face when choosing to postpone
having children. [2 ]

3.4 inhertance
Udertadig Applicatio
 Mendel discovered the principles o inheritance
 Inheritance o ABO blood groups.
with experiments in which large numbers o
 Red-green colour-blindness and hemophilia as
pea plants were crossed.
examples o sex-linked inheritance.
 Gametes are haploid so contain one allele o
 Inheritance o cystic brosis and Huntingtons
each gene.
disease.
 The two alleles o each gene separate into
 Consequences o radiation ater nuclear
diferent haploid daughter nuclei during meiosis.
bombing o Hiroshima and Nagasaki and the
 Fusion o gametes results in diploid zygotes nuclear accidents at Chernobyl.
with two alleles o each gene that may be the
same allele or diferent alleles.
 Dominant alleles mask the efects o recessive skill
alleles but co-dominant alleles have joint efects.  Construction o Punnett grids or predicting the
 Many genetic diseases in humans are due to outcomes o monohybrid genetic crosses.
recessive alleles o autosomal genes.  Comparison o predicted and actual outcomes
 Some genetic diseases are sex-linked and some o genetic crosses using real data.
are due to dominant or co-dominant alleles.  Analysis o pedigree charts to deduce the
 The pattern o inheritance is diferent with pattern o inheritance o genetic diseases.
sex-linked genes due to their location on sex
chromosomes.
 Many genetic diseases have been identied in
nature of ciece
humans but most are very rare.  Making quantitative measurements with
replicates to ensure reliability: Mendels genetic
 Radiation and mutagenic chemicals increase
crosses with pea plants generated numerical data.
the mutation rate and can cause genetic
disease and cancer.

168
3 . 4 i N h E r i TAN CE

Mendel and the principles of inheritance


Mendel discovered the principles of inheritance
with experiments in which large numbers of pea
plants were crossed.
When living organisms reproduce, they pass on characteristics to their
ospring. For example, when blue whales reproduce, the young are
also blue whales  they are members o the same species. More than
this, variations, such as the markings on the skin o a blue whale, can be
passed on. We say that the ospring inherit the parents characteristics.
However, some characteristics cannot be inherited. S cars seen on the
tails o some blue whales caused by killer whale attacks and cosmetic
surgery in humans are examples o this. According to current theories,
acquired characteristics such as these cannot be inherited.
Inheritance has been discussed since the time o Hippocrates and earlier.
For example, Aristotle observed that children sometimes resemble
their grandparents more than their parents. Many o the early theories
involved blending inheritance, in which ospring inherit characters
rom both parents and so have characters intermediate between those o  Figure 1 Hair styles are acquired
their parents. S ome o the observations that biologists made in the rst characteristics and are ortunately not
hal o the 1 9th century could not be explained by blending inheritance, inherited by ofspring
but it was not until Mendel published his paper E xperiments in Plant
Hybridization that an alternative theory was available.
Mendels experiments were done using varieties o pea plant, each o
which reliably had the same characters when grown on its own. Mendel
careully crossed varieties o pea together by transerring the male pollen
rom one variety to the emale parts in fowers o another variety. He
collected the pea seeds that were ormed as a result and grew them to
nd out what their characters were. Mendel repeated each cross with
many pea plants. He also did this experiment with seven dierent pairs
o characters and so his results reliably demonstrated the principles o
inheritance in peas, not j ust an isolated eect.
In 1 866 Mendel published his research. For over thirty years his ndings
were largely ignored. Various reasons have been suggested or this. One
actor was that his experiments used pea plants and there was not great
interest in the pattern o inheritance in that species. In 1 900 several
biologists rediscovered Mendels work. They quickly did cross-breeding
experiments with other plants and with animals. These conrmed that
Mendels theory explained the basis o inheritance in all plants and animals.

Replicates and reliability in Mendels experiments


Making quantitative measurements with replicates to ensure reliability: Mendel's
genetic crosses with pea plants generated numerical data.
Gregor Mendel is regarded by most biologists as characteristics such as red or white fower colour
the ather o genetics. His success is sometimes that can easily be ollowed rom one generation
attributed to being the rst to use pea plants to the next. They can also be crossed to produce
or research into inheritance. Peas have clear hybrids or they can be allowed to sel- pollinate.

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In act Mendel was not the rst to use pea cross pollinating peas:
plants. Thomas Andrew Knight, an English pollen from another plant is dusted on
horticulturalist, had conducted research at to the stigma here
D ownton C astle in Hereordshire in the late
1 8th century and published his results in the
Philosophical Transactions o the Royal S ociety.
Knight made some important discoveries:
pollen is collected
 male and emale parents contribute equally to from the anthers
the ospring;
 characters such as white fower colour
that apparently disappear in ospring can
reappear in the next generation, showing that
lower petal
inheritance is discrete rather than blending;  called the keel
 one character such as red fower colour self pollinating peas:
can show a stronger tendency than the  if the ower is left untouched, the anthers
alternative character. inside the keel pollinate the stigma
 Figure 2 Cross and sel pollination
Although Mendel was not as pioneering in his
experiments as sometimes thought, he deserves (a) Prediction based on
blending inheritance
credit or another aspect o his research. Mendel
was a pioneer in obtaining quantitative results and tall plants 3 dwarf plants
in having large numbers o replicates. He also did
seven dierent cross experiments, not just one.
Table 1 shows the results o his monohybrid crosses.
pea plants with an
It is now standard practice in science to include intermediate height
repeats in experiments to demonstrate the (b) Actual results
reliability o results. Repeats can be compared to
tall plants 3 dwarf plants
see how close they are. Anomalous results can be
identied and excluded rom analysis. S tatistical
tests can be done to assess the signicance o
dierences between treatments. It is also standard
pea plants as tall
practice to repeat whole experiments, using a as the tall parent
dierent organism or dierent treatments, to test
 Figure 3 Example o a monohybrid cross experiment. All the
a hypothesis in dierent ways. Mendel should
hybrid plants produced by crossing two varieties together
thereore be regarded as one o the athers o had the same character as one o the parents and the
genetics, but even more we should think o him character o the other parent was not seen. This is a clear
as a pioneer o research methods in biology. alsifcation o the theory o blending inheritance

Paental plants hybid plants Ofsping om sel-pollinating te ybids ratio
Tall stem  dwar stem All tall 787 tall : 277 dwar 2.84 : 1
Round seed  wrinkled seed All round 5474 round : 1850 wrinkled 2.96 : 1
Yellow cotyledons  green cotyledons All yellow 6022 yellow : 2001 green 3.01 : 1
Purple fowers  white fowers All purple 705 purple : 224 white 3.15 : 1
Full pods  constricted pods All ull 882 ull : 299 constricted 2.95 : 1
Green unripe pods  yellow unripe pods All green 428 green : 152 yellow 2.82 : 1
Flowers along stem  fowers at stem tip All along stem 651 along stem : 207 at tip 3.14 : 1

 Table 1

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3 . 4 i N h E r i TAN CE

Gamete
Gametes are haploid so contain one allele o each gene.
Gametes are cells that fuse together to produce the single cell that is the
start of a new life. They are sometimes called sex cells, and the single cell
produced when male and female gametes fuse is a zygote. Male and female
gametes are different in size and motility. The male gamete is generally
smaller than the female one. It is usually able to move whereas the female
gamete moves less or not at all. In humans, for example, the sperm has a
much smaller volume than the egg cell and uses its tail to swim to the egg.
Parents pass genes on to their offspring in gametes. Gametes contain
one chromosome of each type so are haploid. The nucleus of a gamete Figure 4 Pollen on the anthers o a fower
therefore only has one allele of each gene. This is true of both male contains the male gamete o the plant. The
and female gametes, so male and female parents make an equal genetic male gametes contain one allele o each o
contribution to their offspring, despite being very different in overall size. the plants

Zygote
Fusion o gametes results in diploid zygotes with two
alleles o each gene that may be the same allele or
diferent alleles.
When male and female gametes fuse, their nuclei j oin together, doubling
the chromosome number. The nucleus of the zygote contains two
chromosomes of each type so is diploid. It contains also two alleles of
each gene.
If there were two alleles of a gene, A and a, the zygote could contain two
copies of either allele or one of each. The three possible combinations are
AA, Aa and aa.
S ome genes have more than two alleles. For example, the gene for
AB O blood groups in humans has three alleles: I A, I B and i. This gives six
possible combinations of alleles:
 three with two of the same allele, IAIA, IB I B and ii
 three with two different alleles, IAIB , I Ai and I B i.

segregation of allele
The two alleles o each gene separate into diferent
haploid daughter nuclei during meiosis.
D uring meiosis a diploid nucleus divides twice to produce four haploid
nuclei. The diploid nucleus contains two copies of each gene, but the
haploid nuclei contain only one.
 If two copies of one allele of a gene were present, each of the haploid
nuclei will receive one copy of this allele. For example, if the two
alleles were PP, every gamete will receive one copy of P.
 If two different alleles were present, each haploid nucleus will
receive either one of the alleles or the other allele, not both. For
Figure 5 Most crop plants are pure-bred strains
example, if the two alleles were Pp, 5 0% of the haploid nuclei would
with two o the same allele o each gene
receive P and 5 0% would receive p.

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The separation o alleles into dierent nuclei is called segregation. It


TOK breaks up existing combinations o alleles in a parent and allows new
Did mendel alter his results for combinations to orm in the ospring.
publication?
In 1936, the English statistician Dominant, recessive and co-dominant alleles
R.A. Fisher published an analysis
o Mendels data. His conclusion
Dominant allele