Oxford Resources for IB

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Oxford Resources for IB

Diploma Programme

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 Service /Science Photo Library; p63(b): Monkey Business Images/Shutterstock; p64:

Bénédicte S alin/Université de Bordeaux Cell and Molecular Imaging Service; p65: Eric

Grave/Science Photo Library; pp66-67: Wolfgang Bettighofer, www.protisten.de; p69:

Prof. Alexandro Bonifaz/ Hospital General de México; p70(a): Biophoto Associates /

Great Clarendon Street, Oxford, OX2 6DP, United Kingdom

Science Photo Library; p70(b): Microsc ape / Science Photo Library; p70(c): Don W.

Fawcett / Science Photo Library; p70(d): Biophoto Associates / Science Photo Library;
Oxford University Press is a department of the University of Oxford. It furthers the

p70(e): Dr Gopal Murti / Science Photo Library; p71(a): Dr Gopal Murti / Science Photo
University’s objective of excellence in research, scholarship, and educ ation by

Library; p71(b): Science History Images/Alamy Stock Photo; p71(c): Dr K ari Lounatmaa /
publishing worldwide. Oxford is a registered trade mark of Oxford University Press

Science Photo Library; p71(d): Microsc ape / Science Photo Library; p71(e): Don W.
in the UK and in certain other countries.

Fawcett / Science Photo Library; p72(t): Heiti Paves/Alamy Stock Photo; P72(m): Dr

© Oxford University Press 2023

s
Gopal Murti / Science Photo Library; p72(b): Dr Gary G augler / Science Photo Library;

p73: Andrew Allott; p75: Frank Fox/Science Photo Library; p76: Han, X., Zhou, Z., Fei, L.

The moral rights of the author[s] have been asserted

et al. Construction of a human cell landsc ape at single-cell level. Nature 581, 303–309

s
First published in 2023 (2020). https://doi.org/10.1038/s41586-020-2157-4; p77(l): Eye of Science/Science

Photo Library; p77(r): D avid Scharf/Science Photo Library; p78: Wolfgang Bettighofer,

All rights reserved. No part of this public ation may be reproduced, stored in a

www.protisten.de; p80(t): Steve Gschmeissner/Science Photo Library; p80(b): Tumor

e
retrieval system, or transmitted, in any form or by any means, without the prior

Cell L ab/Phanie/Science Photo Library; p81: Xiao C, Kuznetsov YG, Sun S, Hafenstein SL,

permission in writing of Oxford University Press, or as expressly permitted by

Kostyuchenko VA, et al. (2009), CC BY 2.5 /Wikimedia Commons; p86: Sergio Azenha/

law, by licence or under terms agreed with the appropriate reprographics rights

Alamy Stock Photo; p88: Centers for Disease Control and Prevention; p92(t): The

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organization. Enquiries concerning reproduction outside the scope of the above

C anadian Press / Alamy Stock Photo; p92(b): Science Source / Science Photo Library;

should be sent to the Rights Department, Oxford University Press, at the address

p93: CDC / Science Source / Science Photo Library; p94(t): Herve Conge, ISM / Science

above.

P
Photo Library; p94(b): Ami Images/Science Photo Library; p95: Bob Blaylock, CC BY-SA

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You must not circulate this work in any other form and you must impose this same 3.0 / Wikimedia Commons; p96: K aj R. Svensson/Science Photo Library; p97(tl):

condition on any acquirer Cburnett, CC BY-SA 3.0 / Wikimedia Commons; p97(tr): Ron Singer, Public domain /

Wikimedia Commons; p97(bl): Dr. Michael M ares/S am Noble Museum; p97(br): Brian

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British Library C ataloguing in Public ation D ata

Gratwicke, CC BY 2.5; p98(t): Agefotostock/Alamy Stock Photo; p98(b): Timothy

D ata available

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Hellum/Alamy Stock Photo; p99: Andrew Allott; p100: RGB Ventures SuperStock/Alamy

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9781382016339 Stock Photo; p101(tl): Mike lane/Alamy Stock Photo; p101(tr): EyeLoveBirds from

Vancouver, C anada, CC BY-SA 2.0 / Wikimedia Commons; p101(b): Corbis; p103: Dept.

9781382016377 (ebook)

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of Clinic al Cytogenetics, Addenbrookes Hospital / Science Photo Library; p104: The

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History Collection / Alamy Stock Photo; p109: M auro Fermariello/Science Photo Library;
10 9 8 7 6 5 4 3 2 1

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pp110-112: Andrew Allott; p114: Andrea Izzotti/Shutterstock; p115(t): Melissa Lutz

Paper used in the production of this book is a natural, recyclable product made from

Blouin; p115(b): Vince F/Alamy Stock Photo; p116(t): NOAA Okeanos Explorer Program,

wood grown in sustainable forests.

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2016 Deepwater Exploration of the M arianas, Leg 3; p116(b): Jen Guyton/Nature Picture

Library; p117(t): Gaertner/Alamy Stock Photo; p117(b): World Meteorologic al

The manufacturing process conforms to the environmental regulations of the

Organization; p118(tl): Nature Picture Library/Alamy Stock Photo; p118(tr): Ausc ape
country of origin.

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International Pty Ltd/Alamy Stock Photo; p118(bl): Alan Jeery/Shutterstock; p118(br):

Printed in Italy by Rotolito SpA Vvvita/Shutterstock; p119(t): Gabor C sorba, Hungarian Natural History Museum (or G.
e
C sorba, HNHM); p119(b): Andrew Allott; p122(t): Andrew Allott; p122(bl): Basic Loc al

Acknowledgements

p
Alignment Search Tool; p122(bm): Ken Griths/Shutterstock; p122(br): Edwin Verin/

The “In cooperation with IB” logo signies the content in this textbook has been
Shutterstock; p123: Andrew Allott; p127(l): M atteo Omied / Alamy Stock Photo; p127(r):

reviewed by the IB to ensure it fully aligns with current IB curriculum and oers high-
v

M artin Fowler/Alamy Stock Photo; p128: Koepi, KP., Deere, K.A., Slater, G.J. et al.

quality guidance and support for IB teaching and learning.

Multigene phylogeny of the Mustelidae: Resolving relationships, tempo and biogeo-

o
graphic history of a mammalian adaptive radiation . BMC Biol 6, 10 (2008). https://doi.

The Publisher wishes to thank the International Bacc alaureate Organization for
i

org/10.1186/1741-7007-6-10; p129: Ger Bosma/Alamy Stock Photo; p132(tl): Didier

permission to reproduce their intellectual property.

Descouens/Wikimedia Commons; p132(tr): Peter C airns/Nature Picture Library/ Science
n

Photo Library; p132(bl): Quartl, CC BY-SA 3.0 / Wikimedia Commons; p132(br): Nature

The Publisher would like to thank the following members of the DP Science 2023
Picture Library / Alamy Stock Photo; p133(t): S andy R ae, CC BY-SA 3.0 / Wikimedia

Research Panel for sharing their insights, expertise, and feedback:

Commons; p133(b): M. G. Harasewych/Oxford University Press; p136: Lauren

B. Jane Taylor, Menna Shawky El Sherbiny, Aura Milena Vera, Jessic a K. Hartman,
Suryanata/Shutterstock; p137(t): PAUL D STEWART / Science Photo Library; p137(b):
U

Nilan A. Senaratna, Joanne Walton, Holly O'Donal Allen, Gavin Terry, Arnavaz
Tony C amacho/Science Photo Library; p138: Andrew Allott; p141: Dora Zett/

Kollah, Amanda Lockhart, Lisa Privitera, Ioannis Papatheocharis, Anastasia

Shutterstock; p142(tl): Steve Huskey, Ph.D.; p142(tr): www.openc age photographer, CC
n

Denisova, Dr. Regina K atz, Srivalli Singh, Emma Nason, Rosanne Jacobs-S arkin,
BY-SA 2.5/Wikimedia; p142(bl): Sklmsta/Wikimedia; p142(br): photowind/

Aditya R ao, M aría Cristina S alvador Crow, Tania M Hodges

Shutterstock; p145(t): AGAMI Photo Agency/Alamy Stock Photo; p145(b): Cyril Ruoso /

The publisher would like to thank the following for permissions to use copyright
Nature Picture Library / Science Photo Library; p146: Diego Delso, CC BY-SA 4.0 /

material:
Wikimedia Commons; p147: Bill Coster/Alamy Stock Photo; p148: George Turner; p149:
o
d

Alfredo Garcia S az/Alamy Stock Photo; p150(t): Ailurus~frwiki, CC BY-SA 4.0 /

Cover: D arrell Gulin/Getty Images. Photos: piv: International Bacc alaureate Organisa-

Wikimedia Commons; p150(b): BrazilPhotos/Alamy Stock Photo; p151: Lee D alton/

tion; p2: Claude Nuridsany & M aria Perennou / Science Photo Library; p3(t): Eye of

Alamy Stock Photo; p152: AGAMI Photo Agency/Alamy Stock Photo; p153: Science
i

Science / Science Photo Library; p3(b): Library of Congress/Science Photo Library; p4:
r

History Images / Alamy Stock Photo; p155(t): Andrew Allott; p155(b): Tanya C Smith/

Hubble, M. Kornmesser/ESA; p5: Andrew Allott; p6(t): oliveromg/Shutterstock; p6(b):

Alamy Stock Photo; p156(t): Don Johnston_MA/Alamy Stock Photo; p156(b): Nick Upton
t

Stephen Barlow; p8(tl): Des C allaghan; p8(tr): © 2020 Spirina, Voronkova and Ignatov;

/ Nature Picture Library / Science Photo Library; p157: M annion PD, Upchurch P, Benson
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p9: Andrew Allott; p10(t): Emilio Ereza/Alamy Stock Photo; p10(b): Thekopmylife/

RB, Goswami A. The latitudinal biodiversity gradient through deep time. Trends Ecol Evol.

Shutterstock; p12(t): M arkus Varesvuo/Nature Picture Library/Science Photo Library;

a

2014 Jan;29(1):42-50. doi: 10.1016/j.tree.2013.09.012. Epub 2013 Oct 17. PMID:

p12(b): Кирилл Уютнов, CC BY-SA 4.0 / Wikimedia Commons; p13: John Thomas/

24139126.; p158(l): Cephas, CC BY-SA 3.0 / Wikimedia Commons; p158(r): Jim

Science Photo Library; p15: Lebrecht Music & Arts/Alamy Stock Photo; p16: Power and
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Rorabaugh/USFWS, Public domain / Wikimedia Commons; p160(l): Frederick William

Syred/Science Photo Library; p17: Science History Images/Alamy Stock Photo; p23:
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Frohawk, Public domain / Wikimedia Commons; p160(r): Natural History Museum,

James King-Holmes/Science Photo Library; p27: PDB ID: 1AOI, DOI Citation: Luger, K.,
x

London, CC BY 4.0 / Wikimedia Commons; p161(t): Science History Images/Alamy Stock

M aeder, A.W., Richmond, R.K., S argent, D.F., Richmond, T.J. doi: 10.2210/pdb1AOI/pdb;

Photo; p161(b): © Ausc ape / ardea.com; p163(t): Minden Pictures/Alamy Stock Photo;

p28: LEE D. SIMON / Science Photo Library; p33: M adprime, CC0 / Wikimedia

p163(b): NASA. Collage by Producercunningham., Public domain / Wikimedia

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Commons; p34: Dr Keith Wheeler/Science Photo Library; p36: Eduard Muzhevskyi/

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Commons; p165: Stephen Barlow; p166: Phil M arsh; pp169-170: Andrew Allott;

Science Photo Library/Getty Images; p37(t): Corbin17/Alamy Stock Photo; p37(b):

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p171(tl): Andrew Allott; p171(bl): Andrew Allott; p171(b): B. Bartel/USFWS & Jitze

NOAA; p38: M. Kornmesser/ESO; p39: Space Science Institute/JPL/NASA; p40:

Couperus, CC BY 2.0 / via Wikimedia Commons; p174(t): M auro Fermariello/Science

Thomas Deerinck, NCMIR/Science Photo Library; p41: M att Heaton/FossilEra; p42:

Photo Library; p174(b): United States Department of Agriculture; p178: ibreakstock/

Andrew Allott; p43: Science Photo Library/Alamy Stock Photo; p44: PDB ID: 1FFK, DOI
v

Shutterstock; p180: RM Floral / Alamy Stock Photo; p185: BGSmith/Shutterstock; p188:

Citation: Ban, N., Nissen, P., Hansen, J., Moore, P.B., Steitz, T.A. doi: 10.2210/pdb1FFK/

Jamie Presland; p190(l): m.pilot/Shutterstock; p190(r): Jiri Hera/Shutterstock; p191: Papa

pdb; p46: Jane Gould/Alamy Stock Photo; p47: GSFC/METI/ERSDAC/JAROS, and U.S./

November CC BY-SA 3.0/Wikimedia Commons; p193: Fuse/Getty Images; p195: RCSB

Japan ASTER Science Team/NASA; p48: Noaa Okeanos Explorer Program/Science Photo

PDB; p199(t): Georgios Kollidas/Shutterstock; p199(b): February 2001, D avid Goodsell,

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Library; p49(t): Ted Kinsman/Science Source/Science Photo Library; p49(b): Dr Yorgos

doi:10.2210/rcsb_pdb/mom_2001_2; p200(t): Glow Images/Getty Images; p200(b):

Nikas / Science Photo Library; p50: Royal Institution Of Great Britain / Science Photo

Andrew Allott; p203: Andrei Lomize, CC BY-SA 3.0/Wikimedia Commons; p204:

Library; p51: © 2004 MBARI; © 2011 MBARI (Kim Fulton-Bennett) p52: Copyright of ZEISS

February 2011, D avid Goodsell, doi:10.2210/rcsb_pdb/mom_2011_2; p206: M ark A.

Microscopy; p54(l): Andrew Allott; p54(r): William Allott; p55(t): © Woods Hole

Herzik Jr. Cryo-electron microscopy reaches atomic resolution. Nature 587, 39-40 (2020).

Oceanographic Institution; p55(m): Professors P. Motta & T. Naguro / Science Photo

doi: https://doi.org/10.1038/d41586-020-02924-y; p207(t): April 2000, D avid

Library; p55(b): Andrew Allott; p56(tl): Andrew Allott; p56(tr): Peter Andrus, CC BY-SA

Goodsell, doi:10.2210/rcsb_pdb/mom_2000_4/; p207(b): Science Photo Library /

4.0 / Wikimedia Commons; p56(b): Wim Van Egmond/Science Photo Library; p57(l):

Alamy Stock Photo; p208(l): John Birdsall Social Issues Photo Library / Science Photo

Jeroen Rouwkema, CC BY-SA 3.0 / Wikimedia Commons; p57(r): Copyright of ZEISS

Library; p208(r): Prostock-studio/Shutterstock; p210: Biophoto Associates / Science

Microscopy; p58(t): imageBROKER/Alamy Stock Photo; p58(b): Volgi archive/Alamy

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Stock Photo; p59: Toyoshi Fujimoto; pp60-61: Ge, P., Scholl, D., Prokhorov, N.S. et al.

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courtesy of Roel Haeren and Hans Vink;

https://doi.org/10.1038/s41586-020-2186-z; p63(t): A. Dowsett, National Infection

Contents

A1.1
C1.1

s
A1.2 Nucleic acids 16
C1.2

C1.3

s
e
A2.1

r
A2.2 Cell structure 49

C2.1
A2.3

P
ecnednepedretni dna noitcaretnI
C2.2

y
l
y

n
ytisrevid dna ytinU

A3.1

A3.2
C3.1

O
C3.2

i
s
A4.1

y
A4.2

C4.1
e
A

p
C4.2
v
C

o
i

B1.1

B1.2
n

D1.1

D1.2
U

D1.3
n

B2.1

B2.2
o
d

B2.3

D2.1
i
r

D2.2
t

D2.3 Water potential 648

o

B3.1
f

B3.2
u

B3.3
noitcnuf dna mroF

D3.1
l

egnahc dna ytiunitnoC

D3.2
O

D3.3
a

B4.1
v

B4.2
E
B

D4.1

D4.2

D4.3

Internal assessment: The scientic investigation 796

D

Index 802

Answers: www.oxfordsecondary.com/ib-science-support

iii
 Introduction

The aim of the International Bacc alaureate biology syllabus is to

combine a conceptual approach to biology, an understanding Leve

l of orga
nizat
ion
Them
e

s
1. Mole
cules

2. Cells

3. Orga
of the nature of science and the development of discipline- nism
s
4. Ecos
ystem
s

resul
ted
in the
rich
biodiv
ersity

s
A of life
on
Earth

specic skills. All of these elements are embedded in specic .

A1.1
Wate
r
A2.1
Origin
s of cells
diver A3.1
sity Diver
A1.2 sity
Nucle [HL
only] of
ic acids A4.1
Evolu

contexts. The syllabus road map is shown in Figure 1.

tion
organ and
isms

speci
ation

e
A2.2
Cell
struc
ture
A3.2
Class
ificati
on
A4.2
Cons
A2.3 ervat
Virus and ion
es cladis of
[HL tics
only]
biodiv
ersity
[HL
only]

Topics are organized into four themes and four levels of

r
B
organization. The theme and level of organization shows B1.1
Carb
ohyd
rates
B2.1
Mem
Form and brane
lipids s and
and
B3.1
Gas
mem
brane
trans B4.1
funct Adap
ion port tation
excha to
B1.2 nge

possible conceptual lenses through which the topics c an be Prote

ins

P
envir
onme
B2.2 nt
Orga
nelles
and

y
B3.2
Trans
comp port
artme
ntaliz B4.2
Ecolo
ation gical

B3.3 niche
Musc s
viewed. Students and teachers are encouraged to personalize B2.3
Cell
le and

motili
ty [HL
speci only]
alizat
ion

their approach to the syllabus. This textbook allows you

l
C

Inter

y
actio C1.1
Enzy

to sequence the course by theme or level of organization.

n and mes
and
C2.1
Chem

n
inter ical
depe meta
nden bolism
ce C3.1
Integr
signa ation
lling of
[HL C4.1
only] Popu
lation
body s
C1.2 syste
Cell ms
respi and
ration comm
C2.2 unitie
It is structured in the same way as the syllabus, with each Neur
al signa
lling
s

C3.2
Defen
C1.3
Photo ce
synth C4.2
esis Trans
fer s
again of
st disea
se

t
energ
y and
matte
r

chapter corresponding to a topic and divided into numbered

O
D

i
understandings. Some understandings will also include D1.1
DNA

D2.1
Cell
and
eplica nucle
tion ar
D3.1
Repr
divisi oduc
on tion
D4.1
chan Natur
ge al
D1.2
Prote
in D3.2

s
reference to the applic ation of skills and the nature of science
selec
Inher tion
D2.2 itance
Gene
synth expre
esis ssion

[HL
only]
D3.3 D4.2
Home Stabi
ostas lity and
is
D1.3
Muta
tions chan
and ge
D2.3
Wate
(NOS). gene
editin
r poten
tial
g

D4.3
Clima

r
te chan
ge

y
e
Figure 1

p
v

Nature of science

o
i

Science has features that make it dierent from other • Patterns and trends
n

pursuits such as the arts, social sciences, mathematics, Recognition of a pattern or trend forms an important

or the study of language. Science has particular part of the scientist’s work whatever the science.
U

methodologies and purposes.

• Hypotheses
n

The eective pursuit of modern scientic work and its Patterns lead to a possible explanation. The

theories depends on the Nature of Science, which c an hypothesis is this provisional view and it requires
o
d

be summarized in the following eleven aspects: further veric ation.

• Observations and experiments

i
r

Sometimes the observations in experiments are • F alsic ation

t
o

unexpected and lead to serendipitous results. Hypotheses c an be proved false using other
a

evidence, but it c an't be proved denitely true. This

• Measurements
f

has led to paradigm shis in science throughout

u

Measurements c an be qualitative or quantitative, but

x

history.

all data are prone to error. It is important to know the

l

limitations of your data. • Models

O

Scientists construct models as simplied explanations

• Evidence

of their observations. Models oen contain

Scientists learn to be sceptic al about their

v

assumptions or unrealistic simplic ations, but the aim

observations and they require their knowledge to be

of science is to increase the complexity of the model,

E

fully supported by evidence.

and reduce its limitations.

iv
• Theories • Global impact of science

A theory is a broad explanation that takes Scientists are responsible to society for the

observed patterns and hypotheses and uses them consequences of their work, whether ethic al,

to generate predictions. These predictions may environmental, economic, or social. Scientic

conrm a theory (within observable limitations) or knowledge must be shared with the public clearly

s
may falsify it. and fairly.

s
• Science as a shared activity

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Scientic activities are oen c arried out in

collaboration, such as peer review of work before

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public ation or agreement on a convention for clear

communic ation.

y
l
governments and international organizations to

Course book denition

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develop challenging programmes of international

n
The IB Diploma Programme course books are resource
educ ation and rigorous assessment.

t
materials designed to support students throughout

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These programmes encourage students across the

their two-year Diploma Programme course of study

i
world to become active, compassionate and lifelong

in a particular subject. They will help students gain an

s
learners who understand that other people, with their

understanding of what is expected from the study of

dierences, c an also be right.

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an IB Diploma Programme subject while presenting

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content in a way that illustrates the purpose and aims
e
The IB Learner Prole
of the IB. They reect the philosophy and approach of

p
The aim of all IB programmes to develop internationally
the IB and encourage a deep understanding of each
v

minded people who work to create a better and

subject by making connections to wider issues and

providing opportunities for critic al thinking.

more peaceful world.

o The aim of the programme is to

i

develop this person through ten learner attributes, as

n

The books mirror the IB philosophy of viewing the

described below.

curriculum in terms of a whole-course approach;

Inquirers: They develop their natural curiosity. They

the use of a wide range of resources, international
U

acquire the skills necessary to conduct inquiry and

mindedness, the IB learner prole and the IB Diploma
n

research and snow independence in learning. They

Programme core requirements, theory of knowledge,

actively enjoy learning and this love of learning will be

the extended essay, and creativity, activity, service
o
d

sustained throughout their lives.

(CAS).

Knowledgeable: They explore concepts, ideas and

E ach book c an be used in conjunction with other
i
r

issues that have loc al and global signic ance. In so

materials and, indeed, students of the IB are required
t

doing, they acquire in-depth knowledge and develop

o

and encouraged to draw conclusions from a variety

a

understanding across a broad and balanced range of

of resources. Suggestions for additional and further

disciplines.
reading are given in each book and suggestions for
f

how to extend research are provided.

Thinkers: They exercise initiative in applying thinking
x

skills critic ally and creatively to recognize and approach

In addition, the course companions provide advice
l

complex problems, and to make reasoned, ethic al

O

and guidance on the specic course assessment

a

decisions.
requirements and on ac ademic honesty protocol.

They are distinctive and authoritative without being

Communic ators: They understand and express
v

prescriptive.
ideas and information condently and creatively in

more than one language and in a variety of modes of

E

IB mission statement
communic ation. They work eectively and willingly in

The International Bacc alaureate aims to develop collaboration with others.

inquiring, knowledgeable and c aring young people

who help to create a better and more peaceful world

Principled: They act with integrity and honesty, with

through intercultural understanding and respect.

a strong sense of fairness, justice and respect for the

To this end, the organization works with schools, dignity of the individual, groups and communities.

v
 They take responsibility for their own action and the footnote for information that is part of a ‘body of

consequences that accompany them. knowledge’. That is, denitions do not need to be

footnoted as they are part of the assumed knowledge.

Open-minded: They understand and appreciate their

own cultures and personal histories, and are open Bibliographies should include a formal list of the

to the perspectives, values and traditions of other resources that you used in your work. ‘Formal’ means

s
individuals and communities. They are accustomed to that you should use one of the several accepted forms

s
seeking and evaluating a range of points of view, and of presentation. This usually involves separating the

are willing to grow from the experience. resources that you use into dierent c ategories (e.g.

e
books, magazines, newspaper articles, Internet-

C aring: They show empathy, compassion and respect

based resources, CDs and works of art) and providing

r
towards the needs and feelings of others. They have

full information as to how a reader or viewer of your

a personal commitment to service, and to act to make

P
work c an nd the same information. A bibliography is

y
a positive dierence to the lives of others and to the

compulsory in the Extended Essay.

environment.

l
What constitutes malpractice?
Risk-takers: They approach unfamiliar situations and

n
M alpractice is behaviour that results in, or may result in,
uncertainty with courage and forethought, and have

you or any student gaining an unfair advantage in one

t
the independence of spirit to explore new roles,

O
or more assessment component. M alpractice includes
ideas and strategies. They are brave and articulate in

i
plagiarism and collusion.
defending their beliefs.

s
Plagiarism is dened as the representation of the ideas
Balanced: They understand the importance of

r
or work of another person as your own. The following

y
intellectual, physic al and emotional ballance to achieve

are some of the ways to avoid plagiarism:

personal well-being for themselves and others.
e

p
●
words and ideas of another person to support one’s
Reective: They give thoughtful consideration to their
v

arguments must be acknowledged

own learning and experience. They are able to assess

o
and understand their strengths and limitations in order ●
passages that are quoted verbatim must
i

to support their learning and personal development. be enclosed within quotation marks and
n

acknowledged

A note on ac ademic
●
email messages, websites on the internet and any
U

other electronic media must be treated in the same

integrity
n

way as books and journals

It is of vital importance to acknowledge and

●
the sources of all photographs, maps, illustrations,

appropriately credit the owners of information when

o

computer programs, data, graphs, audio-visual and

d

that information is used in your work. Aer all, owners

similar material must be acknowledged if they are

of ideas (intellectual property) have property rights.

i

not your own work

r

To have an authentic piece of work, it must be based

t

●
when referring to works of art, whether music, lm
on your individual and original ideas with the work of
o

dance, theatre arts or visual arts and where the

others fully acknowledged. Therefore, all assignments,
a

creative use of a part of a work takes place, the

written or oral, completed for assessment must use your
f

original artist must be acknowledged.

u

own language and expression. Where sources are used

x

or referred to, whether in the form of direct quotation

Collusion is dened as supporting malpractice by

or paraphrase, such sources must be appropriately

l

another student. This includes:

O

acknowledged.
a

●
allowing your work to be copied or submitted for

How do I acknowledge the work of others? assessment by another student

v

The way that you acknowledge that you have used the
●
duplic ating work for dierent assessment

ideas of other people is through the use of footnotes

components and/or diploma requirements.
E

and bibliographies.

Other forms of malpractice include any action that gives

Footnotes (placed at the bottom of a page) or endnotes

you an unfair advantage or aects the results of another

(placed at the end of a document) are to be provided

student. Examples include, taking unauthorized

when you quote or paraphrase from another document

material into an examination room, misconduct during

or closely summarize the information provided in

an examination and falsifying a CAS record.

another document. You do not need to provide a

vi
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s
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s
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e
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l
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r

y
e

p
v

o
i
n

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U

n
o
d

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f

u
x

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 How to use this book

The aim of this book is to develop conceptual understanding, aid in skills

development and provide opportunities to cement knowledge and

s
understanding through practice.

s
Feature boxes and sections throughout the book are designed to support these

e
aims, by signposting content relating to particular ideas and concepts, as well as

opportunities for practice. This is an overview of these features:

r
P
Developing conceptual understanding

y
l
Guiding questions

n
t
At the start of every chapter, guiding questions are included to engage you

O
with some of the questions that might arise as they study the material.

i
s
r
Linking questions

y
e
At the end of each section, you will nd examples of linking questions

p
followed by examples of extended-response questions. The linking
v

questions help you view the course content through a dierent lens from

the themes and levels of organization that guide the syllabus.

o
i
n

Nature of Science
U

These illustrate NOS using issues from both modern science and science
n

history, and show how the ways of doing science have evolved over the

centuries. There is a detailed description of what is meant by NOS and the

o
d

dierent aspects of NOS on page iv.

i
r

Theory of knowledge
o

This is an important part of the IB Diploma course. It focuses on critic al

f

thinking and understanding how we arrive at our knowledge of the world.

x

The TOK features in this book are modelled on the TOK Exhibition and pose
l

questions for you that highlight these issues.

O

a
LHA

Content listed under the SL/HL heading should be learned by all students.
v

Sections marked as additional higher level are required for HL students only.
E

viii
Developing skills

ATL Approaches to learning

s
The approaches to learning (ATL) framework seeks of ve general skill c ategories: thinking skills,

to promote skills that will support your learning communic ation skills, social skills, research skills and

s
processes in a way that is useful to all of your IB self-management skills. Throughout the text, there

e
subjects and in your ac ademic c areer following are a number of examples of how the biology course

your study of the IB. The framework consists c an support ATL skill development.

r
P

y
Application of skills

l
Throughout the IB biology syllabus, "Applic ation of that c an be modified and combined to c arry out

n
skills" items are intended to expose you to a range of investigations of your own design. A culminating

t
experimental and mathematic al techniques as well as experience as an IB biology student is an open-ended

O
some suggestions for how technology c an support inquiry c alled the internal assessment investigation.

i
inquiry. A subset of these skills has been designated There is a separate chapter at the end of the book to

s
as "Practising techniques". These are intended guide you through this task.

r
to introduce you to a range of possible protocols

y
e

p
v

o
Practicing
i
n

Data-based questions
U

Frequent examples of data-based questions have processing and analysis. In this syllabus, relatively
n

been included, both embedded within chapters more topic statements focus on presentation and

as well as at the end of chapters. M any of these mathematic al analysis of data generated from
o
d

questions come from previous IB exams. D ata-based experiments.

questions teach the skills of data presentation,

i
r

t
o

a
f

End-of-chapter questions
u
x

Use these questions at the end of each theme to draw together concepts from that chapter and other parts of

the book, and to practise answering exam-style questions. M any of these are past IB biology exam questions.
l
O

a
v

Activity
E

These give you an opportunity to apply your biology knowledge and skills.

ix
 Unity and

s
d i v e rs i t y

s
e
r
1 Molecules

y
l
Common ancestry has given living organisms many shared

n
features while evolution has resulted in the rich biodiversity of

t
life on Earth. Some organisms are adapted to life in water while

O
i
others (such as xerophytic plants) can adapt to the extreme

s
absence of water. All life evolved to be reliant on the unique

r
properties of water. The cytosol inside cells is a water-based

y
medium. Some organisms have unique adaptations related to
e

p
the properties of water.
v

Pond skaters, or water striders (family Gerridae) ican stand

o
i

or move on the surface of pond water. Pond skaters move by

n

making rowing motions with their middle legs, laid at on the

water. The hindlegs steer the creature while the forelegs are
U

used for catching prey. They oen jump considerable distances,

n

but never break the surface of the water. Their bodies are

covered with silver, water-repellent hairs. This particular life

o
d

pattern is an adaptation to the water surface niche.

i
r

Liquid water is essential to all known life forms on Earth. Even

t

the helical structure of DNA is determined by the interaction

o

with water. The hydrophilic (water-loving) sugar–phosphate

f

backbone is found on the outside of the molecule. The

u
x

hydrophobic (water-hating) bases are found on the inside.

l
O

a
v
E
A1.1 Water

What physic al and chemic al properties of water make it essential for life?

s
s
Water bears (Macrobiotus sapiens) are tiny invertebrates that

live in aquatic habitats such as on damp moss. They require

e
water to obtain oxygen by gasexchange. In dry conditions,

they c an enter a shrivelled dormant state tosurvive.

r
What is the longest period of time a water bear c an remain

y
dormant? Toremain alive, what is the minimum metabolic

activity they mustperform?

l
y
When space scientists look for evidence of life on other

n
planets, why do they begin by searching for the presence of

t
liquid water? What are the physic al and chemic al properties of

O
water that make it essential forlife?

i
s
▴ Figure 1 The water bear (Macrobiotus sapiens) in its

r
active state

y
e

p
What are the challenges and opportunities of water as a habitat?
v

o
Aer hunting and killing a whale, whalers processed the
i

c arc ass for oil, blubber and meat. Which orders of mammals
n

have blubber? What role does blubber play in buoyancy?

Do birds or whales require more energy to counteract

gravity? Do organisms require more energy to move through

U

water than through air? What role does blubber play in

n

thermoregulation? What is the signic ance of the high thermal

conductivity of water for warm-blooded animals? What is

o
d

the adaptive advantage of the thorough vascularization of

the blubber? What other adaptations do whales have for the

i
r

unique demands of life in an aquatic environment?

t
o

▴ Figure 2
f

u
x

SL and HL AHL only

l

A1.1.1 Water as the medium for life A1.1.7 Extraplanetary origin of water on E arth and
O

A1.1.2 Hydrogen bonds as a consequence of the polar covalent reasons for its retention

bonds within water molecules A1.1.8 Relationship between the search for
v

A1.1.3 Cohesion of water molecules due to hydrogen bonding and extraterrestrial life and the presence of water

consequences for organisms

E

A1.1.4 Adhesion of water to materials that are polar or charged and

impacts for organisms

A1.1.5 Solvent properties of water linked to its role as a medium for

metabolism and for transport in plants and animals

A1.1.6 Physic al properties of water and the consequences for

animals in aquatic habitats

3
 Unity and diversity

A1.1.1 Water as the medium for life

In 1871, Charles D arwin wrote about the rst organisms appearing “in some

warm little pond”. It is still thought that life began in water; however, most

hypotheses today place the rst cells in the oceans rather than a pond.

s
During the formation of the rst cells, a small volume of water bec ame enclosed

s
in a membrane. Substances were dissolved in this water and chemic al reactions

could occur between the solutes. Aer billions of years of evolution, most

e
molecules of life are still dissolved in water. With water in a liquid state, molecules

r
c an move around and interact, allowing the processes of life to happen.

y
l
y

n
t

O
i
s
r

y
e
▸ Figure 3 Water vapour has been

p
detected in the atmosphere of K2-18b, a
v

planet 110million light years away in the

o
constellation Leo. Water in a liquid state is
i

regarded as essential for the evolution of life

on any planet
n

C
U

A1.1.2 Hydrogen bonds as a consequence

n

of the polar covalent bonds within water

molecules
o
d

In a water molecule, there are covalent bonds between oxygen and hydrogen
i
r

atoms. The sharing of electrons in these bonds is unequal so they are polar
t

covalent bonds. This is bec ause the nucleus of an oxygen atom is more attractive
o

to electrons than the nucleus of a hydrogen atom (Figure 4).

a
f

small negative charge (δ ) on the oxygen atom

x

tends to
l
O

pull the –

δ
a

O
O electrons

slightly + +
δ δ
v

H H
in this

H H
direction
E

+
partial positive charge (δ )

on each hydrogen atom

▸ Figure 4 Polarity of water molecules

Unequal sharing of electrons in water molecules gives the hydrogen atoms a partial

positive charge and the oxygen atom a partial negative charge. The molecules

are bent rather than linear, so the two hydrogen atoms are on the same side of the

molecule and form one pole. The oxygen atom forms the opposite pole.

4
 Molecules

Positively charged particles (positive ions) and negatively charged particles (negative

water
ions) attract each other and form ionic bonds. Water molecules only have partial

molecule
charges, so the attraction is small—but it is enough to have signicant eects. The

attraction between two water molecules is called a hydrogen bond although, strictly

speaking, it is an intermolecular force rather than a bond. A hydrogen bond is the

s
force that forms when a slightly positive hydrogen atom in one polar molecule is
hydrogen

attracted to a slightly negative atom of another polar molecule.

s
bond

e
Although a hydrogen bond is a weak intermolecular force, water molecules are +
δ
δ

small and so there are many of them per unit volume of water. As a result, there
O H

r
are also large numbers of hydrogen bonds (Figure 5) which collectively give
+
δ

H
water its unique properties. These properties are very important to living things.

y
+
δ δ

H O

l
Applying techniques: Demonstrating the strength

y
+

n
H δ
of the hydrogen bond

t
δ
Assemble the apparatus as in Figure 6, with:

O
+
δ H O

i
3

• 10 cm syringe held upside down in a clamp

s
+
H δ

• weights hanging from the barrel of the syringe

▴ Figure 5 Hydrogen bonds between

y
• a tube connected to the nozzle of the syringe
water molecules c an be represented
e
with a dotted or dashed line, whereas
• a gate clip that c an be used to close the tube.

p
covalent bonds within water molecules are
v

1. Keep the gate clip open and the syringe empty.

represented with a continuous line

o
Begin unweighted and add weights one by one
i

until the syringe plunger is pulled down to the

end of the barrel (100 g ≅ 1 N). How much force

n

is needed to overcome the friction between the

plunger seal and the inner surface of the barrel?

U

2. Repeat step 1 with the syringe half-lled with air

n

and the gate clip tightly closed. How much force

▴ Figure 6

is needed to increase the volume of air in the

o
d

syringe to 10 cm ?
i

3. Repeat step 1 with the syringe half-lled with water and no air bubbles. Be
r

c areful to avoid accidents due to heavy weights falling. How much force
t
o

is needed to increase the volume of water to 10 cm ?

a
f

u
x

A1.1.3 Cohesion of water molecules due

l
O

to hydrogen bonding and consequences

a

for organisms
v

There is a mutual attraction between water molecules and hydrogen bonds form
E

between them. Energy is required to break these bonds. In simple terms, water

molecules stick together. The scientic term for this property is cohesion. Living

organisms use this property. Two examples are the conduction of water in xylem

and the use of water surfaces as a habitat.

5
 Unity and diversity

Conduction of water under tension in xylem

Cohesion allows the transport of water under tension in plants. Water is sucked

upwards from the roots to the leaves along tubular vessels in xylem tissue. There

are continuous columns of water in these vessels. E ach column of water is under

s
tension (pulling forces), like a rope pulled at both ends in a “tug of war ”. Tension

in the roots is generated by attractions between soil particles and water. Tension

s
in the leaves develops as water is lost by evaporation to the atmosphere; it is also

e
due to attractions between water molecules and the cell walls of leaf cells. Water

moves upwards bec ause the pulling forces in the leaves are greater than the

r
Figure 7 The rope in a tug of war
forces in the roots.

has to be strong enough to withstand

P
Water in xylem c an withstand tensions bec ause hydrogen bonds make it

y
considerable tension forces

cohesive. As long as the water column remains continuous, it will be pulled

l
upwards. For a column of water in a xylem vessel to break, many hydrogen bonds

y
must be broken simultaneously at one point along the vessel. This takes more

n
energy than is normally available—hydrogen bonds c an withstand surprisingly

t
large tensions. If there were fewer hydrogen bonds, columns of water in xylem

O
would break more easily and trees would not be able to grow so tall.

i
s
Use of water surfaces as habitats

r
The surface of a pond or other body of water acts like an elastic membrane that

y
shrinks to the minimum possible area. This is bec ause water molecules are much
e

p
more attracted to each other by hydrogen bonding than to air particles. This

eect is known as surface tension. All liquids have this property but only a few
v

(such as mercury) have stronger surface tension than water.

o
i

Bec ause of surface tension, it is possible to oat objects such as steel pins on the
n

surface of water, even though they are denser and we might expect them to sink.

This is bec ause cohesion between water molecules due to hydrogen bonds is
U

greater than attractions between water and the oating object. For an object to
n

break through the surface of the water, many hydrogen bonds must be broken

simultaneously. The energy to do this may not be available.

o
d

Living organisms make use of this property by using water surfaces as a habitat.

Water striders (also known as pond skaters) walk on the water surface with their six
i
r

legs. Mosquito larvae live just below the surface, hanging from it using their siphon.
t
o

a
f

u
x

l
O

a
v
E

▴ Figure 8 The ra spider Dolomedes mbriatus hunts prey on the water surface. It detects

prey by means of vibrations passing through the water. It has a coat of unwettable hairs that

help it to remain on the surface, even though its mass is about 30 g and it is denser than water

6
 Molecules

Data-based questions: Tall trees

The tallest trees in the world currently are redwoods 4. At pressures below −2.0 MPa, columns of water in

(Sequoia sempervirens) in Humboldt Redwoods State xylem are prone to breaking. This limits the maximum

s
Park, C alifornia. Researchers climbed ve of these trees, height of trees. Use the data in the graph to predict

including Hyperion which is 116 m tall (the tallest in the a maximum height for redwood trees in Humboldt

s
world). They measured the pressure within xylem tissue State Park. Explain your answer. [2]

in small side branches at dierent heights during the dry

e
season (late September to early October). In Figure 9,

0.4

r
the upper group of data points represents measurements

taken before dawn. The lower group represents

0.6

P
apM / erusserp

y
measurements taken at midday.

0.8

1. a. In this research, height above ground was the

l
independent variable. Explain what makes it an 1.0

n
independent variable. [1]

1.2

b. Xylem pressure was the dependent variable.

t
m e l yx

O
Explain what makes it the dependent variable. [1] 1.4

i
2. a. State the relationship between height above
1.6

s
ground and xylem pressure before dawn. [1]

1.8

y
b. Suggest reasons for the relationship. [2]

2.0
e
3. a. Compare and contrast the pre-dawn xylem

p
30 60 90 120

pressures with the pressures at midday. [2]

height above ground / m
v

o
b. Suggest a reason for dierences. [1]
▴ Figure 9 Source: Koch, G. et al. The limits to tree height. Nature 428,
i

851–854 (2004). https://doi.org/10.1038/nature02417

n

Communic ation skills: Responding to

U

ATL
n

command terms

If a question asks you to “suggest”, you need to propose a solution,

o
d

a hypothesis or another possible answer. You may propose a range of

hypotheses but this does not mean that every answer is a good one. The data
i
r

usually gives clues as to what is possible. Bec ause you are “suggesting”, your
t

statements should be possible and testable. However, they do not need to be

o

proven by the available data.

f

u
x

A1.1.4 Adhesion of water to materials that are

l
O

polar or charged and impacts for organisms

a

Hydrogen bonds c an form between water and the surface of a solid composed
v

of polar molecules. This c auses water to stick to the surface of the solid and is

c alled adhesion. It c an also c ause movement, as when water is drawn through

E

narrow glass tubes. This is c alled c apillary action. The change from air-lled to

water-lled results in formation of many hydrogen bonds, so there is a release

of energy. As air is replaced by water along the tube, many hydrogen bonds are

formed between glass and water, so energy is released. Porous solids such as

paper have large amounts of surface area attractive to water. This means they c an

exert strong suction forces through adhesion. We observe this when water is

drawn through the narrow spaces between cellulose molecules in paper towels.

7
 Unity and diversity

Water is attracted to many chemic al substances in soil. If soil is porous, water is

drawn by c apillary action through dry soil, wetting it. This is how water c an rise up

from an underground source, even though gravity tends to pull it down.

C apillary action due to adhesion is useful in plants. Water adheres to cellulose

s
molecules in cell walls, so any wall that starts to dry out is automatic ally rewetted

as long as there is a source of water available.

s
• If water evaporates from the cell walls in leaves and is lost to the atmosphere,

e
adhesive forces c ause water to be drawn out of the nearest xylem vessel.

This keeps the walls moist so they c an absorb c arbon dioxide needed for

r
photosynthesis. It also generates the low pressures that draw water up in

xylem vessels.

y
• If a xylem vessel becomes air-filled, adhesion between water and the wall

l
of the vessel c an help the vessel to refill with water. For example, the xylem

y
vessels in deciduous trees are air-filled through the winter. In spring, c apillary

n
action due to adhesion helps the sap to rise, refilling the vessels.

O
i
s
100 µm

y
e

p
v

o
i
n

C
U

1 mm
n

▴ Figure 10 Some mosses have narrow hair-like structures on their stems, c alled paraphyllia. The cellulose cell

walls of these structures attract water from fog or dew and store it, helping to keep the moss hydrated. The moss
o
d

on the le is Dicranum majus. The moss on the right (at higher magnic ation) is Climacium dendroides, with

paraphyllia around a group of developing leaves

i
r

t
o

Measuring variables: Determining wet and dry mass

f

u
x

Natural sponge is the so skeleton of animals c alled

◂ Figure 11 In

1665, Robert Hooke sponges (phylum Porifera). The skeleton is composed of

l

published a drawing of
O

the protein spongin, which unusually contains iodine.

a

the structure of natural

Spongin is resistant to digestion by most proteases and

sponge. He described
water adheres to it. Bec ause it has a porous structure and
v

it as “A confus’d heap

large surface area, natural sponge c an absorb and hold

of the brous parts

large amounts of water. This is why it has been used over

E

curiously jointed and

thousands of years for washing and other daily tasks.

implic ated. The joints

More recently, articial sponge has almost entirely

are for the most part

replaced natural sponge. This has similar properties but

where three bres onely

reduces the need for harvesting of wild sponges from

meet, for I had very

seldom met with any marine ecosystems. But ‘sponges’ made of plastic could

that had four ” c ause harm to ocean ecosystems in another way.

8
 Molecules

s
s
e
r
P

y
l
y

n
t

O
i
s
r

y
▴ Figure 12 Image of natural sponge made using a Meiji microscope and
e an iPhone in

2021 (more than 350 years aer Hooke’s drawing)

p
If you c an, obtain a sample of n a t u ra l sponge from 3. Find the mass of each dry sponge.
v

o
a sustainable source and compare it with some

4. Allow the sponges to soak up as much water

i

sy n t h e t i c s p o n g e.

as they can.
n

1. Examine the structures using a microscope.

5. Find the mass of each saturated sponge.

2. Dry the sponges—for example, by placing them in

6. C alculate the amount of water retained by each

U

an oven at 80°C for 24 hours.

sponge as a percentage of the dry mass.

n
o
d

A1.1.5 Solvent properties of water linked to

i
r

its role as a medium for metabolism and for

t
o

transport in plants and animals

a
f

When substances such as sugar dissolve, the particles of the substance become
u

separated and dispersed into a liquid. The liquid is the solvent and the separated
x

particles are solutes. The mixture of solvent and solutes is a solution.

l
O

Water has important solvent properties. The polar nature of the water molecule
a

means that it forms shells around both charged and polar molecules. This
v

prevents them from clumping together so they remain in solution. Water ’s

partially negative oxygen pole is attracted to positively charged ions and its
E

partially positive hydrogen pole is attracted to negatively charged ions, so both

dissolve. Water forms hydrogen bonds with polar molecules.

9
 Unity and diversity

All substances that dissolve in water are hydrophilic (literally, “water-loving”).

These substances include both polar molecules such as glucose and particles

with positive or negative charges, such as sodium and chloride ions. The term

“hydrophilic” is used to describe substances that are chemic ally attracted to

water. Substances that water adheres to but does not dissolve—for example,

s
cellulose—are also hydrophilic.

s
Other substances are hydrophobic. Although this term literally means “water-

e
fearing”, these substances are not repelled by water. They are simply not

attracted by it; instead, they are more attracted to other hydrophobic substances.

r
Molecules are hydrophobic if they are non-polar and they do not have negative
▴ Figure 13 Several plants that c an survive

almost complete dehydration are c alled or positive charges. Hydrophobic substances are insoluble in water although

y
resurrection plants. Rehydration involves they may dissolve in other solvents such as propanone (acetone). All lipids are

water being drawn rapidly through the

hydrophobic, including fats and oils.

l
desicc ated cell walls, by c apillary action.

y
In summary, water dissolves many dierent substances. However, it is not a
Selaginella lepidophylla is an example: the

n
dry ball of the plant swells and opens out in universal solvent bec ause there are also many substances that do not dissolve

t
a few hours, aer which it turns green again in it. Water ’s solvent properties allow it to be used as a medium for metabolism

O
and starts to grow
and for transport.

i
s
Metabolism

r
Cytoplasm is a complex mixture of dissolved substances. It is an aqueous solution,

y
because the solvent is water. The solutes in this aqueous solution can move
e

p
around and interact. Dissolved enzymes catalyse specic chemical reactions. The

many dierent chemical reactions catalysed in cytoplasm are collectively known

v

as metabolism. Without water, the components of these reactions could not move

and come together on the active sites of enzymes. Therefore, water is the medium
o
i

for metabolism.
n

Transport
U

Substances c an be transported as an aqueous solution in both plants and

n

animals. Plants have two such transport systems:

• Mineral ions are transported in xylem sap.

o
d

• Sucrose and other products of photosynthesis are transported in phloem sap.

i
r

Blood transports a diverse range of substances. For example:

t
o

• Sodium chloride is an ionic compound that is freely soluble in water; it

a

dissolves to form sodium ions (Na ) and chloride ions (Cl ), which are c arried
f

in blood plasma.
u
x

• Amino acids have both negative and positive charges. Bec ause of this

they are soluble in water. Their solubility varies depending on the variable
l
O

part of the molecule, which is hydrophilic in some amino acids and

a

hydrophobic in others. All amino acids are soluble enough to be c arried

dissolved in blood plasma.

▴ Figure 14 Hospital patients are oen
v

given uid intravenously. Sometimes the

• Gl u c o s e is a po l a r mo l e c u l e. It is f re e l y s o l u bl e in water so is also c arried

uid is just “saline”, which is water with

E

in pl a s ma .

sodium chloride dissolved in it. Other

patients are given water containing all the • Oxygen is a non-polar molecule, composed of two oxygen atoms and

nutrients they need; this is known as total

sometimes c alled dioxygen. The small size of this molecule allows it

parenteral nutrition (TPN). An emulsier is

to dissolve in water sparingly. Water becomes saturated with oxygen

required in TPN. C an you explain why?

10
 Molecules

at relatively low concentrations. As the temperature of water rises, the

solubility of oxygen decreases, so blood plasma at 37°C c an hold much

less dissolved oxygen than plasma at 20°C or lower. Blood plasma c annot

transport enough oxygen around the body to provide for aerobic cell

respiration. This is why red blood cells contain haemoglobin. H aemoglobin

s
has binding sites for oxygen and greatly increases the c apacity of the blood

to transport oxygen.

s
• F at molecules are entirely non-polar and are larger than oxygen so they are

e
insoluble in water. They tend to coalesce to form large droplets in blood. To

prevent this, small fat droplets are coated in a single layer of phospholipids.

r
Phospholipid molecules are hydrophilic at one end and hydrophobic at the

y
other. This means they c an prevent contact between water and fat, allowing

the small fat droplets to remain suspended in blood plasma while being

l
transported around the body.

n
t

O
A1.1.6 Physic al properties of water and the

i
s
consequences for animals in aquatic habitats

r
A physic al property is a characteristic of a material that c an be observed or

y
measured without changing its chemic al structure. Water has some distinctive
e
physic al properties, with major consequences for living organisms.

p
v

Buoyancy

When an object is immersed in a uid, the uid exerts an upward force on the
o
i

object. This force is equal to the weight of the uid displaced by the object. It is
n

c alled buoyancy. If the density of the object is lower than the density of the uid,

the force acting on the object due to buoyancy will be greater than the force due
U

to gravity and the object will oat. If the density of the object is higher, buoyancy
n

will be less than gravity and the object will sink.

The densities of living tissues are quite variable—for example, bone is denser than
o
d

water while lung tissue and adipose tissue for fat storage are both less dense than

water. However, living organisms have an overall density close to that of water.
i
r

This makes it easier for them to use water as a habitat, bec ause they do not need
t

to use much energy to oat at a particular depth. Bony sh have an air-lled swim
o

bladder which they use to control their overall density. Cyanobacteria have gas

vesicles which they use to adjust how close to the surface they oat.
f

u
x

Air is much less dense than living organisms and provides negligible amounts of

buoyancy. Organisms therefore have to generate li to stay airborne.

l
O

Viscosity

In simple terms, viscosity is the stickiness of a uid which determines how easily it
v

c an ow. Organic solvents such as propanone have low viscosity, whereas treacle

has high viscosity. Viscosity is due to internal friction c aused when one part of
E

a uid moves relative to another part. For example, when a uid ows through

a tube, the velocity is greater in the centre of the tube than at the edges, so

there is internal friction. The more viscous a uid, the greater the friction and the

resistance to ow.

11
 Unity and diversity

Pure water has a higher viscosity than organic solvents, bec ause hydrogen

bonds c ause internal friction. Solutes increase the viscosity even further, so blood

does not ow as easily as water. Seawater has a higher viscosity than freshwater

bec ause of the dissolved salts, with consequences for organisms that swim in

it. The viscosity of air is about 50 times smaller than that of water at the same

s
temperature.

s
Thermal conductivity

e
The rate at which heat passes through a material is known as thermal conductivity.

Water has a relatively high thermal conductivity. F ats and oils conduct heat

r
about 25% as quickly as water, and air 5%. These materials are therefore useful as

heat insulators. On the other hand, aquatic warm-blooded animals are at much

y
greater risk of the loss of body heat than land-based warm-blooded animals.

Water is useful when there is a need to absorb and transfer heat. For example, the

l
high water content of blood allows it to c arry heat from parts of the body where

n
it is generated (such as contracting muscles) to parts that need more heat or parts

t
that are able to dissipate excess heat to the environment.

O
i
Specic heat

s
The heat required to raise the temperature of 1 g of a material by 1°C (or kelvin, K)

−1 −1

is its specic heat c apacity. The specic heat c apacity of water is 4.18 J g K .

y
−1 −1

For air, the value is only 1.01 J g K

e

p
Water has a relatively high specic heat c apacity bec ause hydrogen bonds
v

restrict molecular motion. For the temperature of water to increase, hydrogen

o
bonds must be broken and energy is needed to do this. This is why a relatively
i

large amount of heat is needed to raise the temperature of water. To cool down,
n

water must lose an equally large amount of energy. As a result, the temperature

of water remains relatively stable compared with air temperatures and aquatic

habitats are more thermally stable than terrestrial habitats. The high specic heat
U

c apacity of water also helps birds and mammals (which are mostly composed of
n

water) to maintain constant body temperatures.

Physic al properties of air

o

and water
d

▴ Figure 15 An adult black-throated loon

(Gavia arctica) has a length of about 65 cm

Dierences between the physic al properties of air and water have major
i

and a wing span of 120 cm

r

consequences for organisms living in dierent habitats. Consider the ringed

t

seal (a mammal) and the Arctic or black-throated loon (a bird). They are both of
o

moderate size and have overlapping habitats. Both spend time on land rearing
a

their young and in the water foraging for food. However, the Arctic loon ies
f

while the ringed seal spends far more time submerged in the water. The energy
x

requirements for movement in these habitats vary due to dierences in buoyancy

and viscosity of the medium. Air is less dense, so it provides far less buoyant
l
O

force. The loon must expend more energy to stay alo than the ringed seal
a

oating in water. Water is more viscous, so the seal must use more energy to

move through it. There is about 800times more drag on a body moving through
v

water than through air at the same velocity.

E

Water has greater thermal conductivity than air so it conducts heat away from

the bodies of submerged animals, while air acts as an insulator. It is therefore

easier for a loon in air to maintain a temperature above that of the environment
▴ Figure 16 A ringed seal (Pusa hispida)

than it is for a ringed seal in water. At the same time, water has a higher specic
peeks its head above water in the Laptev

Sea near Russia. A ringed seal rarely grows heat c apacity so it resists changes in temperature. Thus it provides a more stable

longer than 150 cm thermal environment for the seal than air does for the loon.

12
 Molecules

LHA
A1.1.7 Extraplanetary origin of water on

Earth and reasons for its retention

There are nearly 1.4 billion cubic kilometres of water on E arth and 98.3% of this

is in a liquid state. The remainder is solid in ice and snow, or gas as water vapour

s
in the atmosphere. It is unlikely that this water was on E arth when the planet

s
was formed, bec ause temperatures would have been above 100°C so water

would have boiled and been lost to space. There are competing hypotheses

e
for the origin of the vast amounts of water on E arth. The most widely supported

hypothesis is that water was delivered to the E arth by colliding asteroids.

r
P
Currently, large asteroids (with a diameter greater than 5 km) only collide with

y
the Earth about once every 20 million years. This rate of bombardment could not

account for all of the water on Earth, especially as a sample of material recently

l
taken from an asteroid and brought back to Earth contained only a small proportion

n
of water. However, there is evidence of much heavier bombardment during the rst

t
few hundred million years aer Earth’s formation. Also, it is likely that asteroids that

O
collided with Earth early in its history contained more water. Asteroids that have

i
been in orbit for billions of years have lost nearly all of their water due to heat from

s
the Sun evaporating the water and gravity being too weak to retain water vapour.

y
When trying to explain how water was retained on E arth aer its delivery
e by

asteroids, two factors are signic ant.

p
• The distance of the E arth from the Sun ensures that sunlight never raises
v

temperatures high enough for water to boil. Liquid water is retained much

more easily than water vapour due to cohesion from hydrogen bonding.

o
i

• Due to its size, the E arth has relatively strong gravity, holding the oceans
n

tightly to its surface and holding gases within the atmosphere. Some

hydrogen and helium esc ape from the atmosphere into space but very little
U

water vapour.
n

There is evidence for the presence of water on M ars but this seems to have
o

disappeared soon aer the planet’s formation. It is thought that most of this water
d

was used in hydration reactions with minerals in M artian rock. On E arth, the

quantities of these minerals were less so surface water was not used up.
i
r

t
o

a
f

u
x

l
O

a
v
E

◂ Fig ure 17 The comet H y a k u t a k e.

Co m e t s a re m o st l y fo rm e d of ice and

dust. T he y have a diameter of a few

k i l o m e t re s and go a ro u nd t he S un in

hi g hl y e l o n ga t e d orbits. Wh e n a comet

a p p ro a c he s the S u n, t he ice v a p or i z e s to

fo rm a tail of ga s and d u st

13
 Unity and diversity
LHA

Data-based questions: Were comets the source of water in E arth’s oceans?

−4

Scientists have analysed the ratio of deuterium to hydrogen (D/H) of water in the Earth’s oceans (1.56 × 10 ). They have

compared it with the same ratio in:

s
• meteorites (asteroids that have passed through the E arth’s atmosphere)

s
• comets originating from the Oort Cloud including Halley’s comet

e
• comets of the Jupiter family including 67P/C-G, which was explored by the Rosetta spacecra.

AE
oB-ela 

eatua 
proton

r
AE 7 00/C
neutron

4

y
ah-a e/P31

G-C/P76
elttu/

drarra G
electron

100 / C
10

B
1 /C

ella /P
1 /C
–3

l
10


1P

eltra /P301
P-M-/P4
y

n
00 / C
t
oitar

O
i
/

s
–4
10

r
E arth Meteorites Comets of the Comets of the

y
from the Asteroid Oort Cloud uiter  amil
e
▴ Figure 18 In this model of a water Belt

p
molecule, one of the hydrogen atoms has a
v

neutron so it is the isotope deuterium. On

E arth, 1 in 6,420 atoms of hydrogen are

o
i

▴ Figure 19 Source: The European Space Agency

deuterium
n

The graph in Figure 19 shows these D/H ratios, arranged on the x-axis according to their distance from the Sun.

Diamond-shaped data points represent measurements from in situ samples; circles show astronomical data,
U

obtainedremotely.
n

1. Look at Figure 19. The y-axis uses a logarithmic sc ale. Outline what is meant by a logarithmic sc ale. [2]

2. Determine the D/H ratio found on Halley’s comet. [1]

o
d

3. The graph shows data for the 11 comets for which a D/H ratio has been measured. Identify how many of

the comets have a D/H ratio that matches that of water on E arth. [2]
i
r

4. The D/H ratio for comet 67P/C-G was measured by the Rosetta spacecra in 2014. Discuss how this ratio
t
o

changes the likelihood that water on E arth was derived from comets. [2]
a

5. Using the data in the graph, discuss whether asteroids or comets are more likely to have been the source
f

of the E arth’s water. [3]

u
x

l
O

a
v
E

14
 Molecules

LHA
A1.1.8 Relationship between the search for

extraterrestrial life and the presence of water

In the fairy tale, Goldilocks and the Three Bears, a young girl tries three bowls

of porridge. She nds one of them too hot and another too cold but the third

s
bowl is just the right temperature. This is used as a metaphor for the habitable

s
zone around a star, oen c alled the Goldilocks zone. Liquid water is essential to

all known life forms on E arth. If a planet is too close to a star, water will vaporize;

e
too far away and water freezes. However, for planets in the Goldilocks zone, the

temperature allows water to exist in a liquid state.

r
P
The loc ation of the Goldilocks zone depends on the size of the star and the

y
amount of energy it emits. It also depends on the size of the planet, which

determines the strength of gravity and the atmospheric pressure. Within our

l
galaxy alone, it is estimated that there are 40billion planets within a “Goldilocks

n
zone”. The more planets there are in the Goldilocks zone around other stars, the

t
greater the chance that extra-terrestrial life has evolved.

O
i
s
▴ Figure 20 Will the porridge in the large

y
e bowl be too hot or too cold?

p
Linking questions
v

o
1. How do the various intermolecular forces of attraction aect biologic al
i

systems?
n

a. Outline how the properties of cohesion and adhesion are important

to living things. (A1.1.3)

U

b. Describe the role of hydrogen bonding in the structure of DNA.

n

(A1.2.6)

c. Explain the importance of hydrophobic interactions in the structure

o
d

of the plasma membrane. (B2.1.2)

i
r

2. What biologic al processes only happen at or near surfaces?

t

a. Outline an example of how the surface of water acts as a habitat.

o

(A1.1.3)
f

b. Describe the role of cell surface receptors in chemic al signalling.

u
x

(C2.1.6)
l

c. Explain the relationship between surface-area-to-volume ratio and

O

materials exchange. (B2.3.6)

a
v
E

15
 A1.2 Nucleic acids

How does the structure of nucleic acids allow hereditary information to be stored?

s
s
All of the information encoded on a computer is ultimately
Character Binary code Character Binary code

e
based on binary code—a code based on two options, 0 and
A 01000001 N 01001110

1. A computer byte is 8 binary digits. Figure 1 shows the letters B 01000010 O 0 1 0 0 1 1 1 1

r
C 01000011 P 01010000
converted to binary code. How would the term “DNA” be

D 01000100 Q 01010001

represented in binary code? Bec ause each digit c an have four

P
E 01000101  01010010

y
values instead of two, DNA codons with three symbols have 64
F 01000110  01010011

possible values, compared with a binary byte which has 256 G 01000111  01010100

l
H 01001000  01010101
possibilities using eight symbols. For this reason, scientists have

y
I 01001001  01010110

n
worked to develop DNA computers.
J
01001010  0 1 0 1 0 1 1 1

K 01001011  01011000

O
L 01001100  01011001

i
M 01001101  01011010

s
▴ Figure 1

y
e
How does the structure of DNA facilitate accurate replic ation?

p
v

Cells divide for the purposes of maintenance, repair, growth and

reproduction. Why must dividing cells produce new DNA? The

o
i

structure of DNA is dependent on complementary base pairing—A is

n

always paired with T and C is always paired with G. Complementarity

guides accurate replication. Chromosomes are mainly composed of

U

DNA. These chromosomes (Figure 2) are seen during the early stages
n

of cell division. The double structure of each chromosome shows

that the DNA has replicated to form two identical strands, known as
o

chromatids. These strands are linked by a region called the centromere.

d

▸ Figure 2 A coloured sc anning electron micrograph of two human chromosomes

i
r

t
o

SL and HL AHL only

a

A1.2.1 DNA as the genetic material of all living organisms A1.2.11 Directionality of RNA and DNA
f

A1.2.2 Components of a nucleotide A1.2.12 Purine-to-pyrimidine bonding as a

x

A1.2.3 Sugar–phosphate bonding and the sugar–phosphate “backbone” of component of DNA helix stability
l

DNA and RNA A1.2.13 Structure of a nucleosome

O

A1.2.4 Bases in each nucleic acid that form the basis of a code A1.2.14 Evidence from the Hershey–

A1.2.5 RNA as a polymer formed by condensation of nucleotide monomers Chase experiment for DNA as the genetic
v

A1.2.6 DNA as a double helix made of two antiparallel strands of nucleotides with material

two strands linked by hydrogen bonding between complementary base pairs A1.1.15 Charga ’s data on the relative
E

A1.2.7 Dierences between DNA and RNA amounts of pyrimidine and purine bases

A1.2.8 Role of complementary base pairing in allowing genetic information to across diverse life forms

be replic ated and expressed

A1.2.9 Diversity of possible DNA base sequences and the limitless c apacity

of DNA for storing information

A1.2.10 Conservation of the genetic code across all life forms as evidence of

universal common ancestry

16
 Molecules

A1.2.1 DNA as the genetic material of all

living organisms

Genetic material is a store of information. If copied, it c an be passed from cell to

cell and also from parent to ospring. Bec ause genetic material is inherited it is

s
sometimes c alled hereditary information. All living organisms use DNA to store

s
hereditary information.

e
The full name for DNA is deoxyribonucleic acid. The other type of nucleic acid is

ribonucleic acid or RNA. Nucleic acids were rst discovered in the cell nucleus,

r
hence the name. They are very large molecules, made from subunits c alled

P
nucleotides which link to form a polymer.

y
▴ Figure 3 The virus shown in the centre

Some viruses use RNA as their genetic material, for example, coronaviruses and
(black structure) uses DNA as its genetic

l
HIV. This observation does not seem to t the theory that genes are made of DNA material. The virus has burst open and its

n
in all living organisms. However, reproduction is a fundamental property of living DNA has spilled out of the polyhedral head,

where it is stored
organisms and viruses cannot reproduce themselves. Instead, they rely on a host cell

O
for this process so they are not considered to be true living organisms. Therefore,

i
they do not falsify the claim that all living organisms use DNA as their genetic material.

s
r

y
A1.2.2 Components of a nucleotide
e

p
Nucleotides consist of three parts:
v

• a sugar, which has five c arbon atoms so is a pentose sugar

o
i

• a phosphate group, which is the acidic and negatively charged part of

nucleic acids
n

• a base that contains nitrogen and has either one or two rings of atoms in its
U

structure.
n

phosphate sugar base

o
d

O
i
r

O
P O CH
2
t

5
o

O
1
a

C C N

4
f

u
x

3 2

OH OH
l
O

▴ Figure 4 Parts of a nucleotide ▴ Figure 5 Simple diagram of a nucleotide

v

Figure 4 shows these parts and how they are linked together to form an RNA
E

nucleotide. The base and the phosphate are both linked by covalent bonds to

the pentose sugar. The ve c arbon atoms in the pentose sugar are numbered,

with the base linked to C1 and the phosphate to C5.

Figure 5 shows a nucleotide in symbolic form, with a circle to represent the

phosphate, a pentagon for the pentose sugar and a rectangle for the base.

17
 Unity and diversity

O
A1.2.3 Sugar–phosphate bonding and

O O
P thesugar–phosphate “backbone” of DNA

O and RNA

s
To link nucleotides together into a chain or polymer, covalent bonds are formed
CH
2

between the phosphate of one nucleotide and the pentose sugar of the next

s
HC CH base nucleotide.

e
Whenever nucleic acids are produced by living organisms, the nucleotides are

HC CH

r
always added to the growing polypeptide in the same way: the phosphate of

the nucleotide being added is linked by a covalent bond to the pentose sugar of
OH
O

y
the previous nucleotide. Linking together nucleotides in this way creates a series

O P O of alternating sugar and phosphate groups, with a chain of c arbon, oxygen and

l
phosphorus atoms covalently bonded together. This chain forms a strong sugar–

y
O

n
phosphate backbone in DNA and RNA molecules that helps to conserve the

sequence of bases.
CH

t
2

O
i
HC CH base

s
A1.2.4 Bases in each nucleic acid that form

HC CH

y
the basis of a code e
OH OH

There are four dierent bases in DNA and in RNA. Three bases are the same but

p
▴ Figure 6 The oxygen atom shown in red
the fourth one diers. All of the bases contain nitrogen—this is why they are oen
v

forms links between the phosphate of one

referred to as nitrogenous bases.

o
nucleotide and the pentose sugar of the
i

next nucleotide E ach nucleotide contains one base so there are four types of nucleotide in DNA
n

and in RNA. Any two nucleotides c an be linked to each other, bec ause the

bases in DNA bases in RNA

phosphate and sugar used to make the bond are the same. Any base sequence
U

is therefore possible along a DNA or RNA molecule and the number of possible
adenine (A) adenine (A)

sequences is almost innite.

n

cytosine (C) cytosine (C)

The sequence of bases is how information is stored. The information is stored in a

guanine (G) guanine (G)

o
d

coded form—this is the universal genetic code that is shared by all organisms.

thymine (T) uracil (U)

i
r

▴ Table 1
t
o

Data-based questions: Bases in DNA

f

u
x

Look at the molecular models in Figure 7 and answer the 3. Identify three similarities between adenine and

following questions. guanine. [3]

l
O

1. State one dierence between adenine and the 4. Compare the structure of cytosine and thymine. [4]
a

other bases. [1]

5. Although the bases have some shared features, each
v

2. E ach of the bases has a nitrogen atom bonded to a one has a distinctive chemic al structure and shape.

hydrogen atom in a similar position (shown lower Remembering the function of DNA, explain why it is
E

le). Deduce how this nitrogen is used when a important for each base to be distinctive. [5]

nucleotide is being assembled from its subunits. [2]

18
 Molecules

Guanine

NH

s
NH

s
N
NH
2

e
Adenine

NH

r
2

P
N

y
N

NH

l
N

n
Cytosine

t
NH
2

O
i
N

s
r
NH

y
O
e
Thymine

p
O
v

NH
o
i
n

NH
O
U

▴ Figure 7
n
o
d

ATL Communic ation skills: Interpreting and evaluating

i
r

information presented in dierent forms

t
o

Figure 7 in the data-based questions shows three dierent representations

a

of e ach base. The rst is a structural formula, the second is a ball and stick
f

model and the third is a space lling model. The command term “evaluate”
u
x

me ans to make an appraisal by weighing up strengths and limitations.

Evaluate e ach type of representation. Which was most useful in answering

l
O

the data-based questions?

a
v

A1.2.5 RNA as a polymer formed by

E

condensation of nucleotide monomers

RNA is a single, unbranched polymer of nucleotides. The nucleotides are

subunits of a polymer, so they are monomers. The number of nucleotides in a

molecule of RNA is unlimited, but they are always linked in the same way, by a

condensation reaction.
▴ Figure 8 RNA polymers c an be represented

using circles, pentagons and rectangles

19
 Unity and diversity

In a condensation reaction, two molecules are combined to form a single

molecule and water is eliminated. Hydroxyl groups (OH) on the phosphate of

one nucleotide and on the pentose sugar of another nucleotide are used. One

of the OH groups is removed entirely. It is combined with the hydrogen from the

other OH, producing water. The remaining oxygen forms a new covalent bond,

s
linking the two nucleotides. This is shown in Figure 9.

s
e
O O

r
O O
P O P O

y
O O

l
CH CH
2 2

y
O O

n
HC CH base HC CH base

O
i
HC CH HC CH

s
OH OH O OH
+ H O
2

y
OH
O
P O
e

p
O
P O
O
v

5’ end

O
CH

o
2

O
3’end
i

CH
2

O HC base
CH
complementary
n

base pairs HC base

CH
P P

HC CH
S A
T S
U

P hydrogen
HC CH
n

OH OH
C
S bonds

P OH OH

C G S

S
o
d

▴ Figure 9 Condensation reaction between two nucleotides

P

T A S
S
i
r

P P
t

A1.2.6 DNA as a double helix made of two

o

P
a

G
S S
antiparallel strands of nucleotides with the
f

P
u

S
T A
S
two strands linked by hydrogen bonding
x

P P

G C between complementary base pairs

S
l

S
O

P
DNA is composed of strands or polymers of nucleotides. The pentose sugar in
a

T
S
S
e ach nucleotide is deoxyribose and the bases are adenine, cytosine, guanine

P P sugar–phosphate
v

and thymine.

S
backbone

P P

A DNA molecule consists of two strands of nucleotides linked to each other

E

S S

by their bases. The links between the bases are hydrogen bonds. Adenine (A)

only forms hydrogen bonds with thymine (T). Guanine (G) only forms hydrogen
S
S G C
3’end

bonds with cytosine (C). This results in complementary base pairing. A and T

complement each other by forming base pairs and similarly G and C complement

5’end

each other by forming pairs.

▴ Figure 10 The double helix

20
 Molecules

The two strands of nucleotides are parallel to each other. However, they run in

opposite directions so they are said to be antiparallel. For this reason, one strand

ends with the phosphate group of the terminal nucleotide while the other strand

ends with a deoxyribose. If the two strands were oriented in the same direction,

the bases would not be able to form hydrogen bonds with each other.

s
DNA molecules usually adopt a helic al shape. A helix is a coiled structure that has

s
a constant diameter of 2 nanometres (2 nm). Bec ause of the two strands, DNA is a

e
double helix. Figure 10 shows its features.

Drawings of the structure of DNA on paper c annot show all features of the three-

r
dimensional structure of the molecule. Figure 11 shows how the structure of DNA

P
c an be represented simply in a diagram.

y
l
covalent bond

y
P

n
Key

– sugar – phosphate
S S

t
P

S
A T

O
i
A C

– nitrogenous bases

P P

s
T G

r
S

y
S
C G
e

p
P P
v

T A
S

o
i
n

P
P

S
U

S
G C
n

P
CH OH
2

5
H
hydrogen bonds are formed
o
d

between two bases

4
1
i

H H
r

▴ Figure 11 Complementary base pairing between the antiparallel strands of DNA

OH
t

3
2
o

OH OH

A1.2.7 Dierences between DNA and RNA

f

ribose
u

There are three important dierences between the two types of nucleic acid:
x

CH OH
2
1. There are usually two polymers of nucleotides in DNA, whereas there is only
5
H
l

O
O

one in RNA. The polymers are often referred to as strands, so DNA is double-
a

4
1

stranded and RNA is single-stranded.

H H
v

2. The four bases in DNA are adenine, cytosine, guanine and thymine. The four OH
3
2

bases in RNA are adenine, cytosine, guanine and uracil, so uracil is present

OH H
E

instead of thymine in RNA.

deoxyribose
3. The pentose sugar within DNA is deoxyribose, whereas the sugar in RNA is

ribose. Figure 12 shows that deoxyribose has one fewer oxygen atom than
▴ Figure 12 Ribose has an OH group and

ribose. The full names of DNA and RNA are based on the type of sugar in an H atom attached to c arbon 2, whereas

them—deoxyribonucleic acid and ribonucleic acid. deoxyribose has two H atoms

21
 Unity and diversity

parental DNA

A1.2.8 Role of complementary base pairing

in allowing genetic information to be

C

C G

C G replic ated and expressed

A T

s
In DNA, adenine c an only pair with thymine and cytosine c an only pair with

guanine. This is complementary base pairing. It allows an exact copy of a DNA

s
G C

T A molecule to be made in a process c alled replic ation. In DNA replic ation, the

e
T A

two strands of the double helix separate. E ach of the original strands serves as a

C G

guide, or template, for the creation of a new strand. The new strands are formed
replic ation fork

r
A T
by adding nucleotides one by one and linking them together.

G C

y
A T

E ach nucleotide that is added must be c arrying the base that is complementary to

G C C

the next base on the template strand. This means the newly synthesized strand on
T A T A

l
T A T A
each of the two template strands should have exactly the same base sequence as

y
C C G

n
the other template strand. Replic ation changes one original DNA molecule into
C

two identic al DNA molecules, each with one strand from the original molecule
G
C G

t
A
and one new strand. This is c alled semi-conservative replic ation.

O
T A

A T

i
A T

A T

A T
Genetic information consists of sections of DNA called genes. Each gene contains

s
information needed for a particular purpose. When the information in a gene has

G C

r
A T an eect on the cell, this is called gene expression. The rst stage in expressing a

y
A T

T A
gene is the copying of its base sequence, but the copy is made of RNA rather than
T A
e
G

G
DNA. Only one of the two DNA strands is used as a template for this. The rules

p
of complementary base pairing are followed but adenine on the template strand
parental new new parental
v

pairs with uracil on the new strand of RNA, rather than thymine. This process of
strand strand strand strand

making an RNA copy of the base sequence of DNA is called transcription.

o
i

▴ Figure 13 Semi-conservative
n

replic ationof DNA

RNA that is produced by transcription may have a regulatory or structural role in

the cell, or it may be used in protein synthesis. To synthesize a protein, the base
U

sequence of the RNA molecule is translated into the amino acid sequence of a

protein. Again, complementary base pairing is involved. Both transcription and

n

translation are more fully described in Topic D1.2

o
d

A1.2.9 Diversity of possible DNA base

i
r

sequences and the limitless c apacity of DNA

t
o

for storing information

a

Genetic information is stored in the base sequence of one of the two strands of a
f

DNA molecule. Any sequence of bases is possible.

x

• There are four possibilities for each base in the sequence—A, C, G or T.

l
O

• There are 4 or 16 possibilities for a sequence of two bases—AA, AC, AG

a

and so on.
v

• There are 4 or 64 possibilities for a sequence of three bases—AAA, AAC,

AAG and so on.

E

• With n bases, there are 4 possible sequences. As n increases, the number

of possibilities becomes immense. With a sequence of just 10 bases, there

are over a million possibilities.

DNA molecules c an be any length, adding to the potential diversity of base

sequences. The range of possible sequences is eectively limitless, which is an

ideal feature for an information storage system.

22
 Molecules

The diameter of a DNA molecule is just 2 nanometres, so immense lengths of

DNA c an be stored in a very small volume. Compared with data-storage systems

devised by humans, DNA is very economic al, both in terms of the space it takes

up and the amount of material used to make it.

s
s
e
r
P

y
l
y

n
t
◂ Figure 14 A sperm is a DNA delivery system. These

O
human sperm cells each contain 3.3 picograms of DNA,

i
with a total length of about 2 metres and over 3 billion base

s
pairs in total. The microscope image has a grid of lines 50

micrometres apart. How long is each sperm and how wide is

y
the head where the DNA is stored?
e

p
Data-based questions: DNA lengths
v

1. In Homo sapiens, the smallest chromosome (and Its genetic

o
material is single-stranded DNA. Suggest
i

therefore the shortest DNA molecule) is the Y one advantage and one disadvantage of this DNA
n

chromosome which has 57,227,415 base pairs. being single-stranded. [2]

Assuming that the human genome has 3.08 billion

4. Bacteria c an store genetic information in small circular

U

base pairs in total, what percentage of this does

DNA molecules c alled plasmids. A plasmid with

n

the Y chromosome contain? [1]

1,440 base pairs has been found in the bacterium

2. The bacterium Carsonella ruddii has just 173,904 Acetobacter pasteurianus. The main chromosome of
o
d

base pairs in its genome, with an estimate of 224 this bacterium has 3.155 Mb (Mb = megabase pairs).

genes. Of these, 194 code for proteins. A surprisingly What is the ratio between the length of the plasmid
i
r

low 7.3% of the bases are guanine. C alculate the and the length of the main chromosome? [2]
t

percentage of bases that are adenine, cytosine and

o

5. C an you nd examples of DNA molecules from

thymine. [3]
a

animals, bacteria, viruses or plasmids that are shorter

3. C anine circovirus has a genome of 2,063 bases with than the examples given here? C an you nd an
f

two protein-coding genes. This type of virus has a example of DNA with less than 7.3% guanine? [2]
x

protein coat that is only 17 nanometres in diameter.

l
O

a
v

A1.2.10 Conservation of the genetic code

across all life forms as evidence of universal

E

common ancestry

The sequence of bases in DNA or RNA contains information in a coded form.

The information is decoded during protein synthesis. Groups of three bases

are c alled codons and have meanings in the code. There are 64 dierent

23
 Unity and diversity

codons, bec ause each base in a codon c an be any of four, so there are 4 × 4 × 4

combinations. E ach of the 64 codons has a meaning:

• most codons specify one particular amino acid

• one codon signals that protein synthesis should start

s
• three codons signal that protein synthesis should stop.

s
Details of the genetic code are described in Topic D1.2

e
It is an extraordinary fact that—with a few minor exceptions—all living organisms

r
and all viruses use the same genetic code. It represents a sort of genetic language.

Humans use many dierent spoken languages, each of which is an eective form

y
of communication. Many dierent versions of a genetic code could be devised

and they would probably function perfectly well, but all life forms use essentially

l
the same version. For this reason, it is called the universal genetic code.

n
The minor exceptions to the universal genetic code found in some organisms are

t
changes to the meaning of one of the 64 codons. In most c ases, one of the three

O
stop codons has changed to code for a specic amino acid instead. Life has been

i
diversifying by evolution over billions of years so it is not surprising that there

s
have been a few very small changes to the genetic code in some organisms. It is

r
noteworthy that the code has changed so little and that all forms of life still speak

y
essentially the same genetic language.
e

p
v

ATL Thinking skills: Evaluating the role of emotions and attitudes in science

o
i

The words below were spoken by M arshall Nirenberg, one with nature is very real and in fact is very true: we
n

who was awarded the Nobel Prize in Physiology or all use the same genetic language.

Medicine in 1968 for his work on the genetic code.

1. Why did the universality of the genetic code have

The nding that the code is universal had a terric such a profound eect on M arshall Nirenberg and
U

philosophic al eect on me. I knew everything about others at the time?

n

evolution at the time, but these ndings were so

2. What are the implic ations of the recognition of the

immediate and so profound, bec ause I understood

unity of life, to scientists and to other people?

o
d

that most or all forms of life on this planet use the

3. Are there other examples of scientic discoveries

same genetic instructions and so we are all related.
i
r

c ausing a profound change in attitudes?

We’re related to all living things and when I c ame in
t

the garden and saw the plants, the squirrels and some
o

4. To what extent do emotional responses such as

of the birds, it really had a profound eect on me,

a

the one described here support or run counter to

which lasts to this day. I think that the feeling of being

stereotypic al representations of scientists?
f

u
x

ATL Thinking skills: Evaluating the role of languages in science

O

A language is a code which ascribes agreed meanings to 3. Esperanto is (see Figure 15) an international language
v

symbols. created by Ludwik Zamenhof in 1887. He hoped that

a universal second language would promote world

1. What are the benets of sharing a common language?
E

peace and understanding. What are the diculties in

2. For scientists, why is the standardization of

creating a new language? Why does Esperanto not

terminology viewed as essential?

persist widely today?

24
 Molecules

ruĝa roza

oranĝa bruna

s
s
flava blanka

e
verda griza

r
P

y
blua nigra

l
y

n
◂ Figure 15 Colours
purpura

in Esperanto

O
i
4. In what ways is language diversic ation and extinction

s
analogous to speciation?

y
e

LHA
A1.2.11 Directionality of RNA and DNA

p
v

The nucleotides within a strand of DNA or RNA are all linked in the same way:

o
the phosphate group of one nucleotide is linked to the pentose sugar of the next
i

nucleotide. As a result, the nucleotides are all orientated in the same way and the
n

strand as a whole has directionality. The two ends of a strand of DNA or RNA c an

be distinguished as shown in Figure 16.

U

• The pentose sugar of the nucleotide at one end of the strand is unlinked.

This is the 3′ terminal bec ause C3 (c arbon atom number 3) in this sugar is
n

available for linkage to another nucleotide.

o

• The phosphate group of the nucleotide at the other end of the strand is
d

unlinked. This is c alled the 5′ terminal, bec ause within a nucleotide the

phosphate group is attached to C5 of the pentose sugar.

i
r

t
o

pentose sugar phosphate

f

at the 3’ terminal at the 5’ terminal

u
x

l
O

antiparallel strands

of DNA
v

5’ terminal ending 3’ terminal ending

with a phospate with a sugar

E

▴ Figure 16

25
 Unity and diversity
LHA

5’ The directionality of RNA and DNA aects processes c arried out by enzymes or

3’

ribozymes:

• replication in which DNA polymerases and other enzymes make copies of DNA

• transcription in which RNA polymerase makes an RNA copy of a DNA base

s
sequence
3’
5’

3’ 5’

s
• translation at a ribosome with an RNA base sequence determining the amino

acid sequence of a polypeptide.

e
direction of

Bec ause of their directionality, DNA and RNA strands and nucleotides must
replic ation

r
5’

be facing in the correct direction for them to t the active sites of enzymes and
3’

ribozymes. For this reason, replic ation, transcription and translation always

y
▴ Figure 17 Replic ation

happen in the same direction.

• In replic ation, DNA nucleotides are always added to the 3′ end of the

l
y
growing polymer of nucleotides. The 5′ phosphate of the free nucleotide is

n
linked to the deoxyribose sugar at the 3′ end of the growing polymer. DNA

t
replic ation is therefore 5′ to 3′

O
i
• In transcription, RNA nucleotides are always added to the 3′ end of the

s
growing polymer of nucleotides. The 5′ phosphate of the free nucleotide

is linked to the ribose sugar at the 3′ end of the growing polymer.

y
Transcription, like replic ation,
e is therefore 5′ to 3′

• In translation, a molecule of RNA c arries the sequence information for making

p
a polypeptide by linking amino acids together. The ribosome that c arries out
v

translation moves along this RNA molecule towards the 3′ end. Translation

therefore works in a 5′ to 3′ direction.

o
i
n

Replic ation

5’ 3’ DNA nucleotides are always added to the 3′ end of the growing polymer of
U

3’ 5’
nucleotides. The 5′ phosphate of the free nucleotide is linked to the deoxyribose
n

3’ sugar at the 3′ end of the growing polymer. DNA replic ation is therefore 5′ to 3′

Both of the strands in DNA are used as templates during replication. The two
o

5’
d

strands are antiparallel. On one strand, 5′ to 3′ assembly of a new strand moves

direction of

in the same direction as the overall process of replication. On the other strand, it
transcription
i
r

moves in the opposite direction. As a result, there are dierences in what happens

▴
t

Figure 18 Transcription

on the two template strands. These dierences are described in Topic D1.1.
o

Transcription
f

RNA nucleotides are always added to the 3′ end of the growing polymer of
x

nucleotides. The 5′ phosphate of the free nucleotide is linked to the ribose sugar at
l

the 3′ end of the growing polymer. Transcription, like replication, is therefore 5′ to 3′

O

Only one of the two strands of DNA is used as a template for making an RNA

transcript. This is always the strand that allows the assembly of the RNA strand to
v

move in the same direction as the overall process of transcription.

E

Translation

A molecule of RNA c arries the sequence information for making a polypeptide

direction of

by linking amino acids together. The ribosome that c arries out translation moves

translation

along this RNA molecule towards the 3′ end. Translation therefore works in a 5′

▴ Figure 19 Translation
to 3′ direction.

26
 Molecules

LHA
A1.2.12 Purine-to-pyrimidine bonding as a

adenine thymine

component of DNA helix stability

The nitrogenous bases in DNA are in two chemic al groups:

s
• Adenine and guanine are purine bases with mole cules that have two rings

cytosine guanine

of atoms.

s
• Cytosine and thymine are pyrimidine bases with molecules that have only

e
one ring of atoms.

guanine cytosine

r
E ach base pair in DNA therefore has one purine and one pyrimidine base. As

a consequence, the two base pairs are of equal width and require the same

y
distance between the two sugar–phosphate backbones in the double helix. This

helps to make the structure of DNA stable and allows any sequence of bases in thymine adenine

l
genes on a DNA molecule.

n
t
▴ Figure 20 Purine bases have two rings
A1.2.13 Structure of a nucleosome

O
and pyrimidine bases have only one

i
The DNA of eukaryotes looks like a string of beads when viewed using an

H1 histone

s
electron microscope. E ach “bead” is a nucleosome. At the core of a nucleosome

are eight histone proteins. Two copies each of four dierent types of histone

r
DNA

y
together make up a disc-shaped structure. The DNA molecule is wound
nucleosome
e
approximately twice around this protein core.

p
An additional histone protein molecule c alled H1 reinforces the binding
v

of the DNA to the nucleosome core. H1 may also help in the packaging of

o
i

chromosomes when a nucleus is preparing to divide. There is a short section of

linker DNA between adjacent nucleosomes.

n

30nm

fibre

Plants, animals and other eukaryotes have nucleosomes. Bacteria do not have
U

nuclei and their DNA is “naked” bec ause it is not associated with histones.
n

▴ Figure 21 Nucleosomes
o
d

Using molecular visualization soware: Visualizing nucleosomes

i
r

Molecular visualization soware can be used to analyse the the association of the protein core with the negatively
t

association between protein and DNA within a nucleosome. charged DNA.

o

1. Visit the protein data bank at www.rcsb.org and

a

search for “human nucleosome structure”.

f

2. Click “3D View”.

x

3. Rotate the molecule to see the two copies of each

l
O

histone protein. In Figure 22, they are identied by

a

the tails that extend from the core. E ach protein has a

tail like this that extends out from the core.

v

4. Note the approximately 150 bp of DNA wrapped

E

nearly twice around the octamer core.

5. Note the N-terminal tail that projects from the histone

core for each protein. Chemic al modic ation of this

tail is involved in regulating gene expression.

6. Visualize the positively charged amino acids on the

▴ Figure 22

nucleosome core. Suggest how they play a role in

27
 Unity and diversity
LHA

A1.2.14 Evidence from the Hershey–Chase

experiment for DNA as the genetic material

From the late 1800s, scientists were convinced that chromosomes played a

role in heredity and that the hereditary material had a chemic al nature. It was

s
known that chromosomes were composed of protein and DNA but it was not

s
clear which of these molecules was the genetic material. Until the 1940s, most

biologists viewed protein as the more likely c andidate, bec ause it contains 20

e
dierent amino acid subunits, whereas DNA has just four types of nucleotide. In

addition, many specic functions of proteins had already been identied. Variety

r
and specicity of function were considered essential for hereditary material.

y
Alfred Hershey and Martha Chase chose to use the T2 bacteriophage to identify the

genetic material. It has a coat composed entirely of protein, with DNA inside the coat.

l
In the 1950s, it was known that a virus can transform a host cell so that it produces viral

n
proteins; for this to happen, viral genes must have been injected into the host cell.

O
In their experiment, Hershey and Chase took advantage of the fact that

i
DNA contains phosphorus but not sulfur while proteins contain sulfur but

s
not phosphorus. They cultured some viruses that contained proteins with

35 32

radioactive ( S) sulfur and other viruses that contained DNA with radioactive ( P)

y
phosphorus. Then they infected
e separate groups of bacteria with the two viruses.

p
For each group of bacterial cells, they used a blender to separate the non-genetic

component of the virus. Then they centrifuged the culture solution to concentrate
v

the cells in a pellet. The cells were expected to contain the radioactive genetic

o
i

component of the virus. Finally, Hershey and Chase measured the radioactivity in

the pellet and the supernatant.

n

C
U

n
o
d

i
r

DNA
t
o

protein
a
f

u
x

l
O

▴ Figure 24 Diagram illustrating the

v

structure of the T2 virus

E

▴ Figure 23 Coloured transmission electron micrograph (TEM) of T2 viruses

(blue) bound to an Escherichia coli bacterium. E ach virus consists of a large DNA-

containing head and a tail composed of a central sheath with several bres. The

bres attach to the host cell surface, and the virus DNA is injected into the cell

through the sheath. It instructs the host to build copies of the virus (blue, in cell)

28
 Molecules

LHA
Data-based questions: The Hershey–Chase experiment

These diagrams show the process of the Hershey–Chase experiment.

35

s
35 radioactive protein ( S) 35

T2 virus with S virus radioactivity ( S)

in its protein coat in supernatant

s
bacterium

bacteria

e
r
P

y
l
y

n
32

radioactive DNA ( P)
T2 virus with virus

t
32

P in its DNA

O
bacterium

i
bacteria

s
r

y
e

p
v

o
32

radioactivity ( P)
i

in pellet

▴
n

Figure 25

Figure 26 shows the results of the experiment.

U

percentage of isotope in supernatant aer 8 minutes agitation

n
tnatanrepus

100%
o
d

80%

60%
i
ni epotosi fo

40%
o

20%
f

0%
%

35 32

S P
x

▴ Figure 26
l
O

1. Distinguish between a supernatant and a pellet. [2]

2. Explain why the genetic material should be found in the pellet and not the supernatant. [2]
v

32

3. State the percentage of P that remains in the supernatant. [1]

E

32

4. Determine the percentage of P that is spun down into the pellet. [2]

5. Discuss the evidence that DNA is the chemic al which transforms the bacteria into infected cells. [3]

29
 Unity and diversity
LHA

Experiments: Use of radioisotopes as research tools

Two atoms are dierent isotopes of the same element counterbalance the repulsive electric force. As a result,

if they have the same number of protons but dierent unstable atomic nuclei release energy in the form of

s
numbers of neutrons in their atomic nucleus. The chemic al radiation as they assume more stable forms. This radiation

properties of an atom are determined by the numbers of c an be detected.

s
protons and electrons—not neutrons—so isotopes of an
For scientists in the 1950s, radioisotopes were a valuable

e
element have the same chemic al properties. However,
research tool. When introduced in minuscule quantities

they may have dierent levels of nuclear stability. For

to biological systems, these unstable variants of common

32

r
example, S has 16protons and 16neutrons and is stable
atomic elements can be traced as they move through

35

but S has 16protons and 19neutrons and is unstable.

biological systems. György Hevesy won the Nobel Prize in

y
Protons are positively charged and repel each other Chemistry in 1943 for pioneering the use of radioisotopes

with an electric al force. However, at very close in biological research. In 1923, Hevesy published the

l
212

distances they attract each other with a nuclear force. rst study using radioactive Pb as a tracer to follow the

n
Certain combinations of protons and neutrons are absorption and translocation of minerals in plants.

unstable bec ause the attractive nuclear force c annot

O
i
s
A1.2.15 Charga ’s data on the relative

y
amounts of pyrimidine and purine bases
e

p
across diverse life forms
v

Before the structure of DNA was known, scientists hypothesized that it would

o
contain a repeating sequence of the four bases. This would mean the four
i

nucleotides occurred in equal numbers. The tetranucleotide hypothesis was

n

formulated in 1910. However, if DNA had a tetranucleotide structure, it would not be

able to vary enough to be the genetic material. This is why scientists thought it was
U

more likely that the 20 amino acids making up proteins were the genetic material.
n

To test the tetranucleotide hypothesis, Erwin Charga and others analysed DNA

samples from a range of species to nd their nucleotide composition. A portion

o
d

of their data is shown in Table 2.

i
r

t
o

Source of DNA Group Adenine Guanine Cytosine Thymine

a

Human M ammal 31.0 19.1 18.4 31.5

f

C attle M ammal 28.7 22.2 22.0 27.2

u
x

S almon Fish 29.7 20.8 20.4 29.1

l

Sea urchin Invertebrate 32.8 17.7 17.4 32.1

O

Wheat Plant 27.3 22.7 22.8 27.1

Yeast Fungus 31.3 18.7 17.1 32.9

v

Mycobacterium Bacterium 15.1 34.9 35.4 14.6

E

tuberculosis

Bacteriophage T2 Virus 32.6 18.2 16.6 32.6

Polio virus Virus 30.4 25.4 19.5 0.0

▴ Table 2

30
 Molecules

LHA
Data-based questions: Charga ’s data

Use the data in Table 2 to answer the following questions. 4. Explain the ratios between the amounts of bases

in eukaryotes and prokaryotes in terms of the

1. Compare the base composition of Mycobacterium

s
structure of DNA. [2]
tuberculosis (a prokaryote) with the base composition

of the eukaryotes shown in Table 2. [2]

5. Explain how these results falsify the tetranucleotide

s
hypothesis. [2]
2. C alculate the base ratio A + G / T + C, for humans

e
and for Mycobacterium tuberculosis. Show your
6. Suggest reasons for the dierence in the base

working. [2]
composition of bacteriophage T2 and the

r
polio viruses. [2]
3. Ev a l u a t e th e claim th a t in the D NA of e u k a r yo te s

y
and p ro k a r yo t e s , the a mo u n ts of adenine and

thy mi n e a re e qu a l and th e amounts of guanine

l
and cytosine a re equal. [2 ]

n
t

O
i
F alsic ation: The nature of the genetic material

s
Knowledge claims are based on evidence gathered Falsiability is the idea that in science we can at least be

y
through the senses. Scientists make observations, certain of what is not the case, by nding a counter-example.

detect patterns and then form generalizations. These Charga’s analysis falsied the tetranucleotide hypothesis
e

p
generalizations are used to draw conclusions about that the four DNA bases occur in equal amounts. The

things that have not yet been observed. This is known Hershey and Chase experiment falsied the hypothesis that
v

as inductive reasoning. The problem with induction is protein is the genetic material. The work of these scientists

o
i

that there is no certainty that the unobserved things will provided certainty of what was not the case.

conform to the generalization; thus, is there anything

n

about the natural world of which we c an be certain when

we have not observed all c ases?

U

Linking questions
o
d

1. What makes RNA more likely to have been the rst genetic material,
i
r

rather than DNA?

t
o

a. Explain the role of enzymes in the cellular processes associated with

a

heredity. (D1.1.8)
f

b. Outline the role of RNA as a c atalyst. (A2.1.6)

x

c. Compare and contrast the structure of DNA and RNA. (A1.2.7)

l
O

2. How c an polymerization result in emergent properties?

a

a. Distinguish between the properties of glucose and starch. (B1.1.5)

v

b. Outline the role of condensation reactions in forming nucleic acids.

(B1.1.2)
E

c. Explain the relationship between the sequence of amino acids and

the structure and function of proteins. (B1.2.10)

31
 Unity and diversity

TOK

How can we know that current knowledge

s
s
is an improvement on past knowledge?

e
Phoebus Levene made signic ant contributions to the Figure 2 shows the results of an experiment c arried out in

development of our understanding of nucleic acids. He 1928 by Griths involving viruses. Injecting mice with the

r
established the existence of the sugar–phosphate backbone rough strain of a virus did not c ause the death of the mice.

y
in nucleic acids; he identied deoxyribose as the sugar in The smooth strain did c ause the death of the mice. The

DNA; and he coined the name nucleotide. heat-killed version of the smooth strain did not c ause

l
death. However, mixing the heat-killed smooth version

y
He also incorrectly stated that DNA was made up of

n
with the living version of the non-deadly rough version

repeating units of the four DNA nucleotides stacked

did c ause death. Somehow the genetic material of the

t
together. This was known as the tetranucleotide hypothesis.

heat-killed version was able to transform the living non-

O
This hypothesis led Levene to state that DNA could not be

i
virulent version to the virulent version. In 1944, Avery,

the hereditary material, bec ause the tetranucleotides were

McC arty and McCleod took the experiment further. From

s
not suciently variable to be the basis of the code for the

Grith’s experiment, they were aware that dead virulent

r
tremendous diversity of life that exists. This idea was widely

y
strains of bacteria could transform living strains to make them

accepted. Instead, proteins were thought to form the

virulent. In dierent experiments, they attempted to establish

e
hereditary material, bec ause they were known to have great

p
what the transforming material was by adding enzymes that

variety of structure.

would break down dierent chemicals to determine if they

v

o
2

i
HN

dGMP dCMP
n

C
HN

NH
2
N

U
O

N
n

O
N
N

N
O
o
d

O P O

O
O

i
r

O
O
t
O

O
P
o

O–

O
P
O
f

u
x

O
l

O
O

P
a

O O
O
O

N
N
N
v

H
2

O
HN
N
E

dTMP dAMP

▴ Figure 1 A tetranucleotide molecule

32
 Molecules

could interfere with the transformation process. They added evidence to establish that the tetranucleotide hypothesis

RNA ase, proteinase and DNA ase. The DNA ase was able to was incorrect. The weight of evidence was beginning to

interfere with the transformation process. This established support the theory that DNA was the genetic material.

that the hereditary material was DNA.

The Hershey and Chase experiment in 1952 showed

s
In 1950, Erwin Charga analysed the nucleotide convincingly that DNA was the genetic material. The

composition of cells from a number of dierent species. He combination of the three experiments was enough to

s
found that the amount of adenine (A) was not equal to the establish that the new knowledge was an improvement

e
amount of guanine (G), and the amount of thymine (T) was upon past knowledge.

not equal to the amount of cytosine (C). This was sucient

r
P

y
l
y

n
t

O
i
s
r

y
e

p
v

o
i
n

C
U

n
o
d

▴ Figure 2 Avery, McCleod and McC arty were aware that heat-killed virulent bacteria
i
r

contained a chemic al that could transform non-virulent bacteria. They worked to identify the
t

transforming chemic al was

o

a
f

u
x

l
O

a
v
E

33
 Unity and diversity

End of chapter questions

1. Table 1 compares the physic al properties of water and air.

s
Property Water Air Condition

s
1 1 1 1

Specic heat 4.18 J°C g 1.01 J°C g 27°C

1 1 1 1

Thermal 0.6 W m K 0.028 W m K 16°C

e
conductivity

r
3 3

Density 1000 kg m 1.225 kg m 15°C; sea level

P
Buoyancy 650 N 0.8 N Assuming a body of volume

y
3

0.0664 m at 15°C

−3 −6

l
Viscosity 0.7978 × 10 Pa·s 18.6 × 10 Pa·s 27°C

n
▴ Table 1

O
a. Specific heat refers to the amount of energy it d. Viscosity is the force per unit area resisting flow.

i
takes to change the temperature of one gram of

i. C alculate the factor by which the viscosity of

s
substance by 1°C.

water exceeds the viscosity of air. [2]

r
i. Identify which substance (air or water) is more

y
ii. Identify the medium that offers the greater

resistant to changes in temperature. [1]

e
resistance to movement. [1]

p
ii. Identify the habitat that would have a more

e. Construct a visual representation that compares the

v

stable thermal environment and discuss the

advantages and disadvantages of air and water as a

o
implic ations of this. [3]

habitat for a flying bird and a swimming seal. [4]

i

b. Thermal conductivity is a measure of the degree to

n

2. Most intertidal animals are adapted to a marine

which the medium is a conductor of heat.

existence. However, during exposure to air at low tide,

i. C alculate the factor by which the thermal they are subjected to the heat stress that is characteristic
U

conductivity of water exceeds the thermal of the terrestrial environment. This c an affect the ability
n

conductivity of air. [2] of intertidal organisms to survive and reproduce.

ii. Identify the medium in which it would be more The limpet Lottia gigantea is an important food source
o
d

difficult for organisms to sustain their internal for shore birds and for subsistence human harvesters. A

temperatures above that of the surrounding study was c arried out to model thermal stress. Some of
i
r

medium. [1] the results are shown in Figure 2.

t
o

c. Buoyancy is a measure of the upward force

a

provided by a medium to counteract gravity. It is

f

a function of the density of the medium and the

u
x

volume of the object.

l

i. Which organism would have to expend more

O

energy to counteract the effects of gravity: a

a

swimming seal or a bird in flight? [1]

v

ii. Suggest a possible relationship between fish

having air bladders and buoyancy. [2]

E

▴ Figure 1

34
 Molecules

A 40 C 40

minimum l et hal te mp er atur e

air

35 35

30 30

25 25

s
20 20

15 15

s
C° / eutarepmet

C° / eutarepmet
10 10

e
5 5

0 0

r
P
B 40 D 40

y
minimum l et hal te mp er atur e water
yd ob

35 35

l
30 30

n
25 25

20 20

O
15 15

i
10 10

s
5 5

y
0 0

0 500 1000 1500 2000 0 500 1000 1500 2000

e

p
da ys da ys
v

▴ Figure 2 Source: J Exp Biol (2006) 209 (13): 2420–2431

o
i
n

a. Compare and contrast the temperature variations 3. Analysis of the base composition of the polio virus

over time between air (graph C) and water shows that it is adenine 30.4%, guanine 25.4%,

(graph D). [2] cytosine 19.5% and thymine 0.0%

U

b. Identify the temperature that is viewed as being a. From this data, what is the evidence that the polio

lethal to limpets (graph A and graph B). [1] virus is

o
d

c. Graph A and Graph B represent the temperature i. an RNA virus [1]

over time in two areas: 0.5 m above the average

ii. single-stranded [1]

i

low level water line and 1.5 m above the average

r

low level water line.

t
o

i. Deduce, with a reason, which graph represents

which position. [2]

f

ii. Deduce which loc ation results in a higher

x

mortality rate due to thermal stress. [1]

l
O

a
v
E

35
 Unity and

s
d i v e rs i t y

s
e
r
2 Cells

y
l
Common ancestry has given living organisms many shared

n
features while evolution has resulted in the rich biodiversity of

t
life on Earth.

O
i
The fundamental unit of life is the cell. All cells come from

s
pre-existing cells. These are the two main propositions of the

y
cell theory.
e

p
Most living organisms are single cells and most of the
v

biomass on E arth is formed from single-celled organisms.

o
i

Even complex multicellular organisms begin their life cycles

n

as single cells: the whole organism is generated by cell

divisions from a single cell. This cell includes the machinery

U

to gather raw materials from the environment and to use

n

these materials to construct a new cell in its own image,

complete with a new copy of its hereditary information.

o
d

All cells store their hereditary information using the same

i
r

linear chemic al code: DNA. The genetic code is described

t
o

as universal bec ause the same code is used across nearly all
a

forms of life.
f

u
x

All cells function as biochemical “factories”, utilizing the same

basic molecular building blocks. All cells use proteins called

l
O

enzymes as catalysts. Each protein is coded for by a specic

gene or set of genes. All cells copy their hereditary information

v

through templated polymerization, transcribing portions of

E

their hereditary information into the same intermediary form

(RNA). All cells translate RNA into protein in the same way.
A2.1 Origins of cells

What plausible hypothesis could account for the origin of life?

s
s
Is there a consensus view of the conditions that existed on the

pre-biotic earth? If there is one, what were these conditions? How

e
do they dier from the conditions that exist today? In what ways

did living things cause some of the changes to conditions on the

r
early earth?

y
Figure 1 shows a cross-section through a fossilized stromatolite,

showing concentric layers of rock (white) and coal-like organic

l
material (black). The layers of organic material were laid down by

n
cyanobacteria (blue-green algae). How far back can such layers

be found? Do they oer conclusive proof of life?

O
i
▴ Figure 1 Cross-section through a fossilized stromatolite

s
r

y
What intermediate stages could there have been between non-living matter and the rst e
living cells?

p
Figure 2 shows a “white smoker” which is a hydrothermal vent. It
v

is not known when or where life on Earth began. However, some

o
i

of the earliest habitable environments may have been submarine

hydrothermal vents. The oldest known fossils providing evidence

n

of microbial life have been found in precipitates associated with

seaoor hydrothermal vents. For the rst living cells to have

U

appeared, catalysis would have to have occurred. What were

n

some of the some of the necessary developments that would

need to have occurred for the rst life to emerge? How might
o
d

hydrothermal events provided the correct conditions for this

emergence?
i
r

▴ Figure 2 A "white smoker" hydrothermal vent

t
o

AHL only
f

A2.1.1 Conditions on early E arth and the pre-biotic formation of c arbon

x

compounds

A2.1.2 Cells as the smallest units of self-sustaining life

l
O

A2.1.3 Challenge of explaining the spontaneous origin of cells

a

A2.1.4 Evidence for the origin of c arbon compounds

A2.1.5 Spontaneous formation of vesicles by coalescence of fatty acids into

v

spheric al bilayers

A2.1.6 RNA as a presumed rst genetic material

E

A2.1.7 Evidence for a last universal common ancestor

A2.1.8 Approaches used to estimate dates of the rst living cells and the last

universal common ancestor

A2.1.9 Evidence for the evolution of the last universal common ancestor in the

vicinity of hydrothermal vents

37
 Unity and diversity
LHA

A2.1.1 Conditions on early Earth and the

pre-biotic formation of c arbon compounds

The Sun formed about 4,500 million years ago, two-thirds of the way through the

time that our Universe has existed. The Earth formed soon aerwards, as gravity

s
caused gas and dust in the early solar system to come together. At rst, there was no

s
life—there was a pre-biotic period in the Earth’s development. Gases accumulated

but in very dierent concentrations to those in today’s atmosphere. Evidence from

e
ancient rocks has helped scientists to describe the pre-biotic atmosphere:

r
• There were only traces of oxygen bec ause it reacted with other elements.

For example, oxygen reacted with iron to produce iron oxide.

y
• Methane concentrations were higher than today due to intense volc anic

l
activity and meteorite bombardment.

n
• C arbon dioxide concentrations were also probably higher due to emissions

from volc anoes.

O
i
Temperatures are likely to have

s
been higher than they are now.

C arbon dioxide and methane are

y
e heat-trapping greenhouse gases

and although the Sun was emitting

p
20% less energy, comet and asteroid
v

impacts will have raised temperatures.

o
Estimates of temperatures on pre-biotic
i

Earth vary widely. It is also uncertain what

n

the pH of the oce ans w as; estimates

range f rom pH 5 to pH 11.

U

The stratospheric ozone layer that

n

currently protects us by absorbing

ultraviolet radiation (UV) would not

o

have existed, bec ause of the lack

d

of oxygen. Without this layer, more

solar UV would have penetrated

i
r

to the E arth’s surface. UV is a high-

t
o

energy form of radiation and provides

a

the activation energy for chemic al

f

reactions. There may also have

▴ Figure 3 An artist’s impression of conditions on Proxima b. This planet orbits our nearest
u

neighbouring star Proxima Centauri, in the habitable zone where water could exist as a been more lightning on early E arth,
x

liquid. What conditions, apart from liquid water, are needed for life to evolve on this planet? triggering other chemic al processes.
l
O

Bec ause of these dierences, reactions that are not possible today may have
a

occurred spontaneously on pre-biotic E arth. As a result, a variety of c arbon

v

compounds may have formed in specialized environments such as hot springs on

land or hydrothermal vents in the oceans. C arbon compounds may have formed
E

in droplets of water in the atmosphere, creating what has been c alled an organic

aerosol haze. These c arbon compounds would then have been deposited by

rainfall into pools, lakes or seas, creating a “soup” of c arbon compounds.

38
 Cells

LHA
There is much uncertainty about conditions on pre-biotic E arth so scientists are

unsure which c arbon compounds may have spontaneously formed. However,

many of the building blocks of life—such as c arboxylic acids, aldehydes, amino

acids and the bases that are part of DNA and RNA—are all possibilities.

s
Once living organisms had evolved, they c aused enormous changes to

conditions on E arth. O ver time, organisms increased the concentration of oxygen

s
in the atmosphere from zero to 20%. They also reduced c arbon dioxide to very

e
low concentrations. As oxygen levels increased, an ozone layer formed, giving

protection against UV. The greenhouse eect was reduced. It is ironic that once

r
living organisms had evolved from non-living matter, the changes that they

c aused probably made it impossible for life to evolve again.

y
l
Data-based questions: Titan’s atmosphere

n
Titan is S aturn’s largest moon. The atmosphere around it formed by processes similar to those on E arth. Table 1 shows

t
the gases that make up more than 1% of the atmosphere at the surface of the E arth and Titan. There is a thick orange

O
smog in Titan’s atmosphere due to ethane, propane, propene and other hydroc arbons.

i
s
G as Titan E arth

y
nitrogen 95% 78% e
methane 4.9% <0.001%

p
v

oxygen 0.0001% 21%

▴ Table 1

o
i
n

1. What are the dierences between the atmospheres

of E arth and Titan? [5]

U

2. What are the reasons for the atmospheres being so

n

dierent? [5]
o
d

▴ Figure 4 Image of Titan taken by NASA’s C assini spacecra

i
r

t
o

A2.1.2 Cells as the smallest units of

f

self-sustaining life
u
x

It is easy to recognize that a crying baby is alive while a lump of rock is not. It is
l

not so easy to dene what life is. It is common to use a checklist of “functions
O

of life” (such as nutrition and respiration). However, these are just processes

required to maintain life, not life itself.

v

A key dierence between living and non-living things is that living things use

energy to keep themselves in a highly ordered state. They are self-sustaining. This
E

highly ordered state would be extremely dicult to achieve starting with non-

living components. A complex device such as a smartphone can be assembled

from individual components and work when it is switched on. In contrast, living

organisms are just too complex. Currently, the only way to produce a living thing is

by reproducing an existing one. Passing on the ability to maintain a highly ordered

state to ospring is a second key dierence between living and non-living things.

39
 Unity and diversity
LHA

An individual organism is certainly alive. Living organisms may be composed of

one cell (unicellular) or many cells (multicellular). To decide whether each cell in a

multicellular organism is alive, or just the whole organism, we c an look at various

types of evidence:

• Individual cells use energy to maintain a highly ordered state.

s
• Some cells in a multicellular organism may stop doing this. These cells are

s
clearly dead, for example, hair cells or cells in the outer layers of skin.

e
• Cells c an divide to produce more cells.

r
• Cells c an be taken from the body and cultured. For example, HeL a cells have

been kept in cultures since 1951.

y
The evidence is strong enough for us to regard cells as living. However, individual

l
cell components are not self-sustaining. For that reason, cells are considered to

▴ Figure 5 The bacteria in this sc anning

n
be the smallest units of self-sustaining life.
electron micrograph have the smallest

genome (473 genes) of any self-replic ating

O
organism. An articial chromosome

i
containing these genes, which have base

A2.1.3 Challenge of explaining the

s
sequences found in Mycoplasma mycoides,

was transplanted into a cell of Mycoplasma

spontaneous origin of cells

y
capricolum whose own DNA had been

According to the theory of spontaneous generation, living organisms c an be

removed. This pared-down bacterium,
e
developed in 2016, enables scientists
formed from non-living matter.

p
to study the roles of genes in cells. The
v

Experiments by Louis Pasteur and other biologists showed that this claim was
function of 149 of the genes is not currently

o
false. Evidence was also gained from Robert Remak’s observational studies of
known. Is this an articial cell or a modied
i

cells in chickens and frogs. He discovered that every cell is formed by division of
natural cell?
n

a pre-existing cell. This principle bec ame an essential part of the cell theory and

from it some remarkable deductions c an be made.

U

Consider the trillions of cells in your body. Each one was formed by division of
n

a pre-existing body cell, starting with a zygote produced when one sperm from

your father fused with an egg from your mother. The sperm and egg cells were
o
d

produced by cell division in your parents. You can trace the origins of all the cells

in your parents’ bodies back to the zygote from which they developed—and so on
i

through many generations of human ancestry. If you accept that humans evolved
r

from pre-existing ancestral species, you can trace the origins of your cells back
o

through vast numbers of generations over thousands of millions of years of life.

a
f

However, life has not always existed on E arth. If you keep going back through the
u

generations, you must eventually reach the earliest cells to have existed. Unless
x

they travelled to E arth from somewhere else in the universe, these rst cells must
l

have developed from non-living material. This deduction leads to a very dicult
O

question: how could a structure as complex as a cell arise from non-living material

by natural means?
v

It is argued that cells are too complex to have arisen by evolution. However, if

there was a series of intermediate stages over a long period of time, evolution of
E

the rst cells becomes more feasible. These are developments required for the

origin of cells:

• c atalysis—to give control over which chemic al reactions occur

• self-assembly—c arbon compounds such as amino acids must assemble to

form polymers

40
 Cells

LHA
• compartmentalization—a membrane must develop to enclose cell contents

• self-replic ation of molecules—as a basis for inheritance and the persistence of

successful variants.

There are hypotheses for how each development could have occurred.

s
s
F alsic ation: The origin of the rst cells

e
Biologists understand that claims in science, including hypotheses and

r
theories, must be testable. Unfortunately, it is very dicult to test hypotheses

relating to the origin of cells, bec ause this happened billions of years ago

y
when conditions on E arth were very dierent. Well-preserved fossils of the

rst protocells are unlikely to be found. Some of the most ancient specimens

l
described as fossils have been re-analysed and found to be crystals. Scientists

n
have attempted to model conditions on pre-biotic E arth but it is not possible

to replic ate with certainty the conditions that would have existed.

O
These diculties do not mean that hypotheses about the origin of cells are

i
untestable and therefore unscientic. Other methods of testing c an be used.

s
Figure 6 3.77 billion year old banded

For example, the genomes of living organisms contain vast amounts of data
iron rock from Isua in western Greenland.

r
and one approach is to examine this data for information about the origins of
Some scientists claim that there are signs

y
the rst cells.
of life in this rock. Others believe that the
e
structures visible could be the result of

p
metamorphosis of sedimentary rocks
v

A2.1.4 Evidence for the origin of c arbon

o
i
n

compounds

In 1929, the biologist J.B.S. H aldane wrote an article on the origin of life. In
U

it, he described the pre-biotic ocean as a “hot dilute soup” in which a variety
n

of c arbon compounds could have formed. He based this hypothesis on an

assumption that the atmosphere contained water vapour, c arbon dioxide

and ammonia. H aldane claimed that: “when ultraviolet light acts on a mixture
o
d

of water, c arbon dioxide and ammonia, a vast variety of organic substances

are made, including sugars and apparently some of the materials from which
i
r

proteins are built up”.

t
o

This hypothesis for the origin of c arbon compounds was tested experimentally
a

in the early 1950s by Stanley Miller and Harold Urey. In a ve-litre ask, they
f

mixed methane, hydrogen and ammonia—the mixture of gases they thought

x

was representative of the pre-biotic atmosphere. They added water vapour to

the mixture by boiling water in another ask, then used electric al discharges
l
O

to simulate lightning. A condenser cooled the substances produced, then the

a

condensate was returned to the ask of boiling water.

v

Aer the experiment had been running for a day, the water turned pink. Aer

a week, it was dark red. Analysis showed that a variety of c arbon compounds
E

had indeed been produced, including more than 20 dierent amino acids.

This showed that it was possible for c arbon compounds to form spontaneously

on E arth before life had evolved, as long as the conditions in the Miller–Urey

apparatus simulated pre-biotic conditions accurately enough.

41
 Unity and diversity
LHA

ammonia

water vapour (NH )

3

electrode
methane (CH )
4

hydrogen

s
(H )
2

s
e
condenser

r
P

y
cold

water in

l
y

n
cooled water containing

t
organic compounds

O
i
s
sample taken for

y
chemical analysis
e
▴

p
Figure 7 Miller and Urey’s apparatus
v

o
i

A2.1.5 Spontaneous formation of vesicles

n

by coalescence of fatty acids into spheric al

▴ Figure 8 Phospholipids naturally

U

bilayers

form spheric al bilayers in water, with the

n

Vesicles are small droplets of uid, enclosed in a membrane. They are very
hydrophilic heads (blue) facing out from the

bilayer and the hydrophobic tails (green) common structures inside cells. Some cells also produce extracellular vesicles,
o
d

forming the core c alled exosomes. Vesicles probably played a part in the early evolution of cells.

The membrane of vesicles is mainly composed of phospholipids. One end of

i
r

a phospholipid molecule is attracted to water (the hydrophilic head) bec ause

t
o

it is polar. The remainder is non-polar (two hydrophobic tails). These tails are
a

more attracted to non-polar substances than to water. A molecule with both

f

hydrophilic and hydrophobic parts is c alled amphipathic.

u
x

When mixed with water, phospholipids naturally assemble into bilayers.

The hydrophilic heads face outwards so they are in contact with water. The
l
O

hydrophobic tails face inwards, away from water. Experiments have shown that
a

these bilayers spontaneously form stable spheric al structures; such structures are

the basis of vesicles.

v

If phospholipids or other amphipathic molecules were part of the “soup”

E

of c arbon compounds on pre-biotic E arth, they would have self-assembled

into bilayers and vesicles would very likely have formed. Movement of polar

molecules into and out of these spheric al structures would have been limited by

the hydrophobic membrane core. As a result, the vesicles could have developed

▴ Figure 9 Butterfat droplets

their own internal chemistry, dierent from that of the surroundings. They would

have been cell-like even though they were not yet proper cells.

42
 Cells

LHA
A2.1.6 RNA as a presumed rst genetic

material

Living organisms today have genes made of DNA and use enzymes as c atalysts.

To replic ate DNA and pass genes to ospring, living organisms need enzymes.

s
However, to make enzymes, they need genes! At an earlier phase in evolution,

s
RNA may have been the genetic material. RNA c an store information in the same

way as DNA but it is self-replic ating and it c an act as a c atalyst.

e
Some viruses (usually considered to be non-living) use RNA as their genetic

r
material. This supports the theory that RNA could have been used before genes

P
made of DNA evolved. Viruses with RNA as their genetic material (for example,

y
coronaviruses) tend to have a very high mutation rate, bec ause the polymerase

enzyme that copies the base sequence is much less accurate than the equivalent

l
enzyme used to copy DNA. This does not matter much in a virus with only a few

n
genes and a high reproduction rate. It may even be an advantage in helping

t
the virus to evade the host’s immune system. However, in a living organism with

O
thousands of genes, genetic stability is much more important so a change to

i
using DNA as the genetic material would have been benecial.

s
Living cells produce hundreds or even thousands of enzymes, all of which are

y
proteins. At one time it was thought that proteins were the only molecules
e
whose three-dimensional structure was complex enough to act as a c atalyst.

p
However, a small number of processes in cells have been found to be c atalysed
v

by RNA. Consider the synthesis of polypeptides in ribosomes. The core of the

o
large subunit of the ribosome is composed of two RNA molecules. Together,
i

these molecules c atalyse the formation of peptide bonds between amino acids.
▴ Figure 10 RNA c an form complex three-
n

This process is repeated many times to produce a polypeptide. RNA c an act as

dimensional shapes, as in this hammerhead

a c atalyst bec ause it c an form complex three-dimensional structures that c an ribozyme which has two loops and three

helices
undergo precise interactions with other molecules.
U

n
o
d

Data-based questions: Protocells

i

A protocell is a compartment enclosed in a phospholipid 1. Protocells lacking RNA were radioactively labelled
r

membrane. Protocells are used to model how more and mixed with unlabelled vesicles that contained
t
o

complex biologic al cells or components of cellular RNA (lower curve in Figure 11) or did not contain RNA
a

organization may have originated. It is likely that (upper curve in Figure 11).
f

protocells existed on pre-biotic E arth, with self-replic ating

a. Compare and contrast changes in the size of
u

molecules enc apsulated by a membrane. It is also

x

the radioactively labelled protocells when they

thought that such structures could grow and divide.

are mixed with vesicles containing RNA and not
l
O

In an experiment, researchers used a simple protocell containing RNA.

a

consisting of a self-replicating RNA molecule encapsulated

b. Suggest what might have happened to make the

by a membrane. For growth to occur, new membrane

v

radioactively labelled protocells become smaller.

material is needed. However, there were no cellular

mechanisms to manufacture new membrane material. It has

E

been hypothesized that protocells containing RNA can grow

by capturing new membrane material from the environment.

43
 Unity and diversity
LHA

a. Analyse the results.

1.3

b. Evaluate the hypothesis that the presence of RNA

a era

inside vesicles increases the likelihood that they will

sllecotorp

1.2
e c af r u s

capture membrane material from other protocells.

s
1.1

1.0

s
evitaler

fo

a era
1.0

e
sllecotorp
e c af r u s
0.9

r
0.9

P
evitaler

y
0 10 20 30 40 50
0.8

fo
time / minutes

l
▴ Figure 11

n
0.7

2. The radioactively labelled protocells were articially

t
swollen, which makes them more likely to c apture

O
0 10 20 30 40 50

i
membrane material from other protocells. They were

time / minutes

mixed with unswollen protocells containing RNA

s
▴ Figure 12 Source of Figure 11 and Figure 12: Chen, I. A., Roberts, R.
(lower curve in Figure 12) or not containing RNA

W., & Szostak, J. W. (2004). The emergence of competition

y
(upper curve in Figure 12).
between model protocells. Science (New York, N.Y.),

305(5689), 1474–1476. https://doi.org/10.1126/

e
science.1100757

p
v

Applying technology: Computer modelling

o
i
n

Using computer modelling to view ribozymes

Visit the RCSB PDB website and search for “ribosome”.

U

Choose an image of the large subunit of the ribosome

n

and view it. You should be able to rotate the image to

investigate its protein and RNA components. There are

o
d

two RNA molecules which together act as a ribozyme:

23S rRNA and 5S rRNA.

i
r

t
o

a
f

▸ Figure 13 In this image, 23S rRNA is shown

u

in green and 5S rRNA is shown in orange

x

l
O

a
v

A2.1.7 Evidence for a last universal common

ancestor
E

Living organisms store information using a genetic code. There are 64 “words”

in the code, c alled codons, and each codon is a sequence of three bases. Every

codon has a specic meaning; it is either an amino acid or a stop or start signal.

It does not matter how meanings are assigned to codons, as long as there is

consistency. The same is true of language—for example, the letters f-i-s-h could

have referred to anything but now have a specic meaning.

44
 Cells

LHA
It would be perfectly possible for dierent species to use dierent genetic codes,

just as humans use dierent languages around the world. However, when the

genetic code was investigated, it was found to be universal—it is the same in all

species, with only a small number of minor variations. The meanings of the 64

dierent codons could be assigned in an almost limitless number of ways, having

s
dierent meanings for dierent species. This makes it highly unlikely that two species

would use the same genetic code by chance. Instead, the obvious explanation for

s
species using the same code is that they inherited it from a common ancestor.

e
It is possible for strikingly similar structures to evolve in organisms that do not have

r
a recent common ancestor. This is called convergent evolution. However, this

is not thought to be the reason for the universal code because living organisms

y
have so many other shared features. For example, key parts of structures within

cells—such as the ribosome and the enzymes that synthesize DNA and RNA—are

l
essentially the same in all organisms. More than 350 widely occurring protein

n
families have been identied in prokaryotes, each with an evolutionary ngerprint

that can be traced back to a common ancestor. The most recent common ancestor

t
to have existed is called LUCA—the last universal common ancestor.

O
i
It is likely that other forms of life evolved. At some stage, however, these life

s
forms bec ame extinct, presumably due to competition from LUCA or species that

r
evolved from LUCA. This is the process of natural selection, which has continued

y
from the rst evolution of life onwards. Figure 14 represents the evolution and
e

p
extinction of life forms over time.
v

o
i
n

C
U

n
o
d

i
r

t
o

◂ Figure 14 On this tree diagram, extinct

LUCA
f

line ages are shown with dotted lines and extant

u
x

line ages with continuous lines. Three origins

of life from non-living matter are shown on this

l

diagram but scientists are not yet sure how many

O

origins there actually were

v

A2.1.8 Approaches used to estimate dates

E

of the rst living cells and the last universal

common ancestor

Palaeontology has p rovi d e d i nv a l u a bl e evidence about th e pa thw ays of

e vo l u ti o n , so it is an o bv i o u s a p pro a c h fo r dating th e f i rs t l i vi n g cells and the

last c o mm o n u n i ve rs a l a n c e s t o r. T h e re a re re l a ti ve l y w e l l - p re s e r ve d ro c k s

45
 Unity and diversity
LHA

da t i n g f ro m 3 .5 to 3 .0 billion ye a rs a go (Gy a ). These ro c k s contain fo ss i l -

like s t r u c t u re s with i s o to pe ra ti o s s u g ge s t i n g they a re th e re m a i n s of l i vi n g

o rg a n i s ms . How e ve r, a l t e r n a ti ve exp l a n a ti o n s h ave be e n s u g ge s te d fo r ma ny

of th e s e s t r u c t u re s . The e arliest u n c o n t e s te d evidence of l i fe comes f ro m

ro c ks in We s te r n A u s tra l i a , k n ow n as the St re l l e y Po o l Fo r m a t i o n . In these

s
ro c ks , l a rg e s tr u c tu re s th a t re s e mb l e fo ss i l i z e d s tro m a t o l i t e s h ave

be e n d i s c ove re d.

s
e
A stromatolite is formed when mats of cyanobacteria in shallow seawater trap

sediments and secrete c alcium c arbonate, slowly building rocky mounds over

r
thousands of years. No other plausible explanation has been proposed for the

Strelley Pool structures, which date from 3.42Gya. This is therefore a minimum

y
date for the earliest cells and for LUCA, based on fossils. However, there are

simpler forms of life than the bacteria that form stromatolites, so we c an deduce

l
that the earliest cells must have existed before 3.42Gya.

n
t

O
i
s
r

y
e

p
v

o
i
n

▸ Figure 15 Stromatolites in shallow water

at Hamelin Pool M arine Nature Reserve,

U

Shark Bay, Western Australia

n

The oldest rocks found on E arth have all been metamorphosed by heat and

pressure, so they do not contain clearly recognizable fossils. The only evidence of
o
d

life that we c an hope to nd comes from isotope ratios. C arbon originating from

13 12

living organisms has a low C/ C ratio. Banded iron rock from Akila and Isua in
i
r

13

west Greenland shows this C depletion and dates from 3.70 to 3.85Gya. These
t

rocks may be the remains of stromatolites; if so, this would push the origin of the
o

simplest cells further back in time.

f

Th e E arth fo r m e d a bo u t 4 .5 Gy a . No ro c k s o l de r th a n a bo u t 4 .0 Gy a re m a i n

x

be c a u s e te c to n i c p ro c e ss e s continuously d e s troy ro c k by s u b du c t i o n

and c re a te n ew ro c k f ro m m a g ma . How e ve r, when ro c k is g ro u n d dow n

l
O

by e ro s i o n , th e h a rde s t f ra g me n t s c an p e rs i s t and become pa r t of n ew

a

13

s e di me n ta r y ro c ks . Zi rc o n pa r t i c l e s w i th depleted C dating f ro m 4 .1 Gy a

13 12

h ave been fo u n d in yo u n ge r ro c k s at Jack Hi l l s , We s te r n A u s tra l i a . The C/ C

v

ra ti o is consistent w i th a bi o g e n i c o r i gi n bu t th i s is far f ro m pro o f of th e

exi s t e n c e of l i fe.
E

Scientists trying to date the origins of life can also analyse genomic information.

The number of dierences between the genomes of two species is proportional

to the time since they diverged from a common ancestor. A recent study using this

approach suggested that LUCA and the rst living cells existed nearly 4.5Gya,

soon aer the Earth is thought to have been impacted by the planet Theia. This

impact would have sterilized the Earth and led to the formation of the Moon.

46
 Cells

LHA
Millions of

years ago

art formed

4,600
by accretion

s
eia impact

s
e
4,000

oldest known rocks

r
P
undisputed evidence

y
3,500

for life

l
life on land

n
3,000

O
oxygen production by

i
potosyntesis

s
2,500

r
▴ Figure 16 S atellite view of Jack Hills, Western Australia, where there are zircon particles

y
dating to 4.4Gya. These are the oldest fragments of the E arth’s crust so far discovered
e

p
v

2,000
A2.1.9 Evidence for the evolution of the

o
i

last common ancestor in the vicinity of

eukaryotes
n

hydrothermal vents

1,500

Even though LUCA probably lived more than 3,500 million years ago (>3.5Gya),
U

it is possible to investigate its genetic make-up using organisms alive today.

n

Researchers have identied genes that occur widely among the groups of

organisms that originated early in the history of life—bacteria and archaea. A wide
1,000
o
d

distribution suggests that these genes were inherited from an early common
algae

ancestor. If an evolutionary tree is constructed for a shared gene and it matches

i
r

the accepted evolutionary tree for bacteria and archaea, deductive reasoning
animals
t

tells us that a gene has been inherited from a common ancestor of bacteria and
500
o

archaea. This suggests that LUCA had the gene.

vertebrates
a
f

Using this technique, researchers have identied 355 protein families that are
u

likely to have been in LUCA’s genome. They are genes needed for anaerobic
x

0 flowering plants

metabolism and for xing c arbon dioxide and nitrogen. From this, we c an
l

deduce that LUCA lived in an environment with high concentrations of hydrogen, ▴ Figure 17 Timeline for life based on
O

evidence from rocks. Most of these dates

c arbon dioxide and iron. These conditions are found in and around hydrothermal

are still hotly debated

vents in the oceans.
v

Hydrothermal vents are cracks in the E arth’s surface, characterized by gushing

E

hot water c arrying reduced (unoxidized) inorganic chemic als such as iron sulde.

There are various types of vent. However, alkaline hydrothermal vents (white

smokers) have conditions most suited to the origin of life. The hydrothermal uids

emerge at temperatures of 60°C to 90°C and contain high concentrations of

hydrogen, methane, ammonia and suldes. These chemic als represent readily

accessible supplies of energy, which early cells would have needed to assemble

c arbon compounds into polymers. C arbon dioxide would also have been

47
 Unity and diversity
LHA

required; this was probably present in much higher quantities at the time when

the rst cells were evolving.

There are still many problems in understanding how the rst cells evolved from

non-living matter. However, it seems likely that hydrothermal vents were the site

s
of this amazing event.

s
e
r
P

y
l
y

n
t

O
i
s
r

y
e

p
▴ Figure 18 K awio Barat is a submarine volc ano o the coast of Indonesia. It has vents

releasing superheated, chemic al-laden water into the ocean at a depth of over a mile.
v

When this superheated water meets the cold surrounding water, minerals are precipitated

producing pale “smoke”. This is why this type of vent

o is known as a “white smoker ”. The

i

minerals form porous deposits and it is in these pores that the rst cells may have evolved
n

from non-living matter, 4.5billion years ago

U

Linking questions
n

1. For what reasons is heredity an essential feature of living things?

o
d

a. Outline the processes that are dependent on cell division. (D2.1.8)

i
r

b. Explain why meiosis is uniquely necessary for sexual reproduction.

t

(D2.1.9)
o

c. Discuss the relationship between heredity and natural selection. (D4.1)

f

2. What is needed for structure to be able to evolve by natural selection?

x

a. Compare discrete and polygenic inheritance. (D3.2.14)

l
O

b. Distinguish between intraspecific and interspecific competition.

a

(C.4.1.10, C4.1.11)
v

c. Discuss the role of diversity in the process of natural selection. (D2.1)

E

48
 A2.2 Cell structure

What are the features common to all cells and the features that dier?

s
s
Figure 1 shows a hot spring extremophile community. This community

thrives in 75°C water in the hills of New Mexico. The community in the

e
picture is made up of sulfur bacteria (purple), algae and protozoa, all

one celled organisms. How does the cell theory take into account the

r
diversity of cell structure? What features of cells are universal? What are

y
some examples of features that are unique to certain cells? What are the

implic ations of the cell theory? What are the limits to what the cell theory

l
predicts or explains?

n
t

O
▴ Figure 1 Sc anning electron

i
micrograph of a hot spring extremophile

s
community

y
How is microscopy used to investigate cell structure?
e

p
The human eye has limited resolving power. What does resolution refer to with
v

respect to optic al devices? What is the actual limit to the resolving power of the

human eye? How does this compare to a bird of prey like an eagle? How large are
o
i

cells? Organelles? Membranes? What is the resolving power of the dierent type of
n

microscopes like light and electron microscopes? A sc anning electron microscope

was used to prepare the image shown in Figure 2, which is an embryo on the head
U

of a pin. What is the value of a SEM over a transmission electron microscope?

n
o
d

▴
i

Figure 2 Coloured sc anning

r

electron micrograph (SEM) of a

t
o

human embryo on the tip of a pin

a

SL and HL AHL only

f

A2.2.1 Cells as the basic structural unit of all living organisms A2.2.12 Origin of eukaryotic cells by endosymbiosis
x

A2.2.2 Microscopy skills A2.2.13 Cell dierentiation as the process for developing
l

A2.2.3 Developments in microscopy specialized tissues in multicellular organisms

O

A2.2.4 Structures common to cells in all living organisms A2.2.14 Evolution of multicellularity
a

A2.2.5 Prokaryote cell structure

v

A2.2.6 Eukaryote cell structure

A2.2.7 Processes of life in unicellular organisms

E

A2.2.8 Dierences in eukaryotic cell structure between

animals, fungi and plants

A2.2.9 Atypic al cell structure in eukaryotes

A2.2.10 Cell types and cell structures viewed in light and

electron micrographs

A2.2.11 Drawing and annotation based on electron

micrographs

49
 Unity and diversity

A2.2.1 Cells as the basic structural unit

of all living organisms

Individual cells are fundamental units of life. Some small organisms consist of

a single cell but larger organisms are multicellular. It has been estimated that

s
13

a 70 kg human consists of 3.8 × 10 cells—that is nearly 40 trillion cells. L arge

s
multicellular organisms have many dierent cell types, each specialized for a

particular role.

e
The statement that living organisms consist of cells is an example of a the ory.

r
This the ory w as develope d when Robert Hooke and other biologists from

P
the 17th century onw ards use d mic roscopes to look at the structure of living

y
organisms. P lant cells are relatively e asy to view with a mic roscope. By the

19th century, animal tissues could also be examine d. Both types of tissue were

l
found to consist of cells. From this, scientists conclude d that all organisms

n
are made of cells. They had not looke d at all parts of all organisms but they

t
had found a trend that allowe d them to make general pre dictions about the

O
structure of organisms.

i
s
▴ Figure 3 Robert Hooke’s drawing of Since the development of the cell theory, researchers have discovered some

cork cells
structures in living organisms that do not consist of typic al cells; some of these

y
structures are described later.e Despite these exceptions, however, the cell theory

is still useful and it has not been rejected. If a new organism is discovered, we c an

p
be reasonably condent that some or all of it will consist of cells.
v

o
i

Observations, theories and inductive reasoning

n

Biologists are interested in the natural world and observations are an example of inductive reasoning—

look c arefully at it—they act as observers and make going from the specic to the general. In the c ase of the
U

observations. Sometimes biologists notice a trend or cell theory, the specic discovery that parts of diverse
n

pattern in their observations and from this they develop organisms consisted of cells led to the generalization that

a general theory. Theories developed from specic all organisms consist of cells.
o
d

Cork
i
r

consists of cells
t
o

Embryos
f

consist of cells
x

All living organisms

consist of cells
l
O

Elder pith
a

consists of cells

Theory developed by
v

inductive reasoning

Toad cartilage
E

consists of cells

Observations

▴ Figure 4 The cell theory was developed by inductive reasoning

50
 Cells

inner layer of tadpole-like larvacean (dwarfed

larvacean house by mucus house it secretes)

s
s
e
r
P

y
l
y

n
t

O
i
s
r

y
e

p
▴ Figure 5 A team of researchers at Monterey Bay Aquarium Research Institute (MBARI), led by K akani K atija, has been researching marine
v

organisms c alled larvaceans. The photograph on the le shows a larvacean’s “house” which consists of two non-cellular mucus structures.

o
The large coarse-mesh outer structure excludes coarse non-food particles. The inner ne-mesh structure c aptures smaller food particles. The
i

larvacean itself is too small to be seen in this image. The photograph on the right shows a magnied view of a larvacean (the blue tadpole-like
n

organism) adjacent to the inner part of its mucus house. By beating its tail, the larvacean pumps water through the inner and outer mucus

lters to extract food particles from the surrounding seawater. The actual organism is about 3 to 5 centimetres long but the non-cellular house

it makes and lives inside c an be up to a metre in diameter. The MBARI research shows there are still exciting discoveries to be made about
U

the natural world. It also shows that there are some exceptions to the theory that living organisms make everything out of cells
n
o
d

A2.2.2 Microscopy skills

i
r

Lenses a l l ow us to look at s tr u c tu re s that a re too s ma l l to see w i th the naked

t
o

e ye — a ny th i n g s ma l l e r than about 0.1 mi l l i m e t re s . A single c o nvex lens is

a

u s e fu l fo r ma gn i f y i n g up to 20 times ( 2 0 × ). How e ve r, th i s is not enough fo r

f

s tu dy i n g th e s t r u c t u re of cells. M i c ro s c o p e s w i th two or mo re lenses make

u

mu c h smaller s t r u c t u re s vi s i bl e be c a u s e the m a g n i fi c a ti o n of th e lenses is

x

mu l ti pl i e d. Fo r ex a m pl e, a 10 × e ye p i e c e lens c o mb i n e d with a 40× h i gh -

l

pow e r o bj e c ti ve lens g i ve s a to ta l ma gn i f i c a t i o n of 400 ×. This a l l ows us

O

to see s t r u c t u re s as small as 0.0 0 0 1 m i l l i me tre s (0.1 mi c ro m e t re s) . Us i n g a

mi c ro s c o p e is an e ss e n ti a l s ki l l fo r b i o l o gi s ts .
v
E

51
 Unity and diversity

Using a light microscope

• If you want to increase the magnic ation, move the

camera

slide so the most promising region is exactly in the

middle of the eld of view and then change to a

s
higher magnic ation lens.

s
eyepiece

Use these hints to troubleshoot when you are focusing:

e
objective lens

Problem Solution

r
stage Nothing is visible M ake sure the specimen is actually

P
when you try to under the lens, by c arefully

y
condenser
fine focus
focus positioning the slide and using low

power rst.

l
light source

coarse focus

n
You c an see a There is an air bubble on the slide.

circle with a thick Ignore it and try to improve your

t
▴ Figure 6 Parts of a light microscope
black rim. technique for making slides so

O
i
there are no air bubbles.
Try to improve your skill at using microscopes as much as

s
you c an.
There are blurred Either the lenses or the slide have

parts of the image dirt on them. Ask your teacher to

r
• Learn the names of parts of the microscope.

y
even when you clean them.
e
• Understand how to focus the microscope to get the
focus it as well as

p
best possible image.
you c an.
v

• Look aer your microscope so it stays in perfect

The image is very Adjust the diaphragm to increase

working order.
o
i

dark. the amount of light passing through

the specimen.
n

• Know how to troubleshoot problems.

The image looks Adjust the diaphragm to decrease

Look aer your microscope by following these guidelines:
U

rather bleached. the amount of light passing through

• Always focus by moving the lens and the specimen

the specimen.
n

further apart. Never move them closer to each other.

▴ Table 1
• M ake sure the upper and lower surfaces of the slide
o
d

are clean and dry before putting it on the stage.

Making temporary mounts of cells and tissues and

using stains
i

• Never touch the surfaces of the lenses with your

r

ngers or anything else. The slides you examine with a microscope c an be

t
o

permanent or temporary. M aking permanent slides is very

a

• C arry the microscope c arefully with a hand under it to

skilled and takes a long time, so these slides are normally

support its weight securely.

f

made by experts. Permanent slides of tissues are made

u

Course and ne focusing

using very thin slices of tissue.
x

• Put the slide on the stage, with the most promising

M aking temporary slides is quicker and easier, so you c an
l

region in the centre of the window in the stage that

O

do this for yourself.

a

the light comes up through.

• Place the cells on the slide, in a layer not more than

• Always focus at low power rst, even if you need high-

v

one cell thick.

power magnic ation eventually.

• Add a drop of water or stain. Stains help structures

E

• Focus with the larger coarse-focusing knobs rst.

that are pale or transparent to show up more clearly.

When you have nearly got the image in focus, use the

• C arefully lower a cover slip onto the drop. Try to

smaller ne-focusing knobs to make it really sharp.

avoid trapping any air bubbles.

52
 Cells

• Remove excess uid or stain by

cover c arefully lower the

putting the slide inside a folded gently squeeze

slip cover slip

to remove excess
piece of paper towel and pressing

fluid
lightly on the cover slip.

s
stain or water

cover slip

s
▸ Figure 7 M aking a temporary mount

e
slide

folded

paper towel

r
Sketches and instructions for six dierent cell types are

shown in Table 2.

y
1 Moss leaf 4 Leaf lower epidermis

l
Use a moss plant with very thin leaves. Mount a Peel the lower epidermis o a leaf. The cell

n
single leaf in a drop of water or methylene blue drawn here was from Centranthus. Mount in

stain. water or in methylene blue.

O
10 µm

20 µm

i
s
r

y
e

p
v

o
i

2 Banana fruit cell 5 Human cheek cell

n

Scrape a small amount of the so tissue from Use a cotton bud to scrape cells from the

a banana and place on a slide. Mount in a drop inside of your cheek. Smear them on a slide

of iodine solution. and add methylene blue to stain.

U

20 µm
o
d

i
r

t
o

10 µm
f

3 M ammalian liver cell 6 White blood cell

x

Scrape cells from a freshly cut surface of liver Smear a thin layer of mammalian blood over a
l

(not previously frozen). Smear onto a slide and slide and stain with Leishman’s stain.
O

add methylene blue to stain.

5 µm
v
E

2 µm

▴ Table 2

53
 Unity and diversity

Observing, drawing and photographing cells Photography is an alternative to drawings. The advantage

of photographs is that they contain real data rather than

When you have focused at high power on plant or animal

one biologist’s subjective interpretation of it. Digital

cells, it is useful to record your observations by drawing a

microscopes are increasingly common and they make it

typic al cell. Alternatively, you could use a smartphone to

s
very easy to take photos.
take a photo through the microscope.

cell cell

s
e
r
bad good bad good bad good

y
▴ Figure 9 Qualities in drawings

l
Measuring sizes using an eyepiece graticule

n
You can measure the actual sizes of structures visible

through a microscope by using a scale inside the eyepiece,

t
called a graticule. The graticule has to be calibrated so

O
i
you know what size each unit on the scale indicates. This

s
will be dierent for each objective lens. For example,

if one unit on the scale represents 2.5micrometres

y
at 400× magnication (high power), it will represent
e
25micrometres at 40× magnication (low power).

p
v

o
i

▴ Figure 8 Onion epidermis cells photographed with a

n

smartphone. Some of the cells have a red pigment in their

cytoplasm. The black-edged circles are air bubbles; this is

U

a common fault in temporary microscope slides. They are a

type of artefact—something not naturally present that was

n

introduced during preparation of the slide

o

A biologic al drawing of a cell is a type of diagram

d

bec ause cell structure is shown with some features

i

only, such as the nucleus. Usually the lines on a drawing

r

represent the edges of structures. Do not show

t
o

unnecessary detail and only use faint shading. The cell ▴ Figure 10 Microscope image photographed using a
a

smartphone, showing a fruit of Centranthus ruber and a graticule

membrane is too thin to see, but you c an deduce its
f

sc ale. 100graticule units = 5millimetres or 5,000micrometres

position and you should include it in your drawing. For
u

example, it forms the outer edge of a blood cell.

x

C alculating actual size, magnication and sc ale

Drawings and diagrams are more informative if they are

l

Structures seen using a microscope appear larger than

O

annotated. Use a ruler to draw a straight line from e ach

they actually are. Most microscopes have more than one

a

structure of interest to a position o the diagram. Then

objective lens, so you c an magnify specimens by dierent

add notes there. You might simply identify the structure

v

factors. A typic al school microscope has three levels of

with a name, or you c an add other details such as the

magnic ation:

function.
E

• 40× (low power)

Drawings of structures seen using a microscope are

larger than the actual size—the drawing shows structures

• 100× (medium power)

magnied. Everything on a drawing should be shown to

• 400× (high power)

the same magnic ation and the magnic ation should be

c alculated and indic ated.

54
 Cells

If you take a photo down a microscope, you c an magnify Sc ale bars may be put on micrographs or drawings, or

the image even more. A photo of a microscope image shown alongside them. A sc ale bar is a straight line,

is c alled a photomicrograph, oen abbreviated to labelled with the actual size that the bar represents. For

micrograph. Electron micrographs are taken using an example, a 10 mm long sc ale bar on a micrograph with a

s
electron microscope. When you draw a specimen, magnic ation of ×10,000 would be labelled 1 µm.

you c an make the drawing larger or smaller, so the

s
magnic ation of the drawing is not necessarily the same as

the magnic ation of the microscope.

e
Worked example

To nd the magnic ation of a micrograph or a drawing,

The length of an image is 30 mm. It represents a

r
you need to know two things: the size of the image (in

structure that has an actual size of 3 µm. Determine the

the drawing or the micrograph) and the actual size of the

magnic ation of the image.

y
specimen. Then you use this formula:

Either:

size of image

l
magnic ation =
−3

30 mm = 30 × 10 m
actual size of specimen

n
If you know the size of the image and the magnic ation,
−6

3 µm = 3 × 10 m

you c an c alculate the actual size of a specimen.

t
−3

30 × 10

O
When using this formula, you must make sure you use the magnic ation = = 10,000 ×

i
−6

3 × 10

same units for the size of the image and the actual size of

s
Or:
the specimen. They could both be millimetres (mm) or

r
micrometres (µm) but they must not be dierent, otherwise

y
30 mm = 30,000 µm

the calculation will be wrong. You can convert millimetres

30,000
e
magnic ation = = 10,000 ×
to micrometres by multiplying by 1,000. You can convert

p
3

micrometres to millimetres by dividing by 1,000.

v

o
i
n

Data-based questions: Size, magnic ation and sc ale

U

1. a. Determine the magnic ation of the

n

Thiomargarita cells in Figure 11. [3]

b. Determine the maximum diameter of the

o
d

whole cell in the micrograph. [2]

◂ Figure 12 Mitochondrion

with false colour (red)

i
r

◂ Figure
t

11 Thiomargarita

3. The magnic ation of the human cheek cell from a

o

cells (one whole cell

a

compound microscope (Figure 13) is 2,000×

and two in part). The

f

a. C alculate the length of a 20 µm sc ale bar on

sc ale bar represents
u

the image. [2]

0.2 µm
x

b. Determine the maximum length of the cheek cell. [2]

l

2. In Figure 12, the actual length of the mitochondrion

O

is8 µm.

a. Determine the magnic ation of the electron

v

micrograph. [2]

◂ Figure 13 Human cheek cell

b. C alculate the length of a 5 µm sc ale bar on

E

stained with methylene blue

this electron micrograph. [2]

4. a. Using the width of the hen’s egg as a guide,

c. Determine the width of the mitochondrion. [1]

estimate the actual length of the ostrich egg in

55
 Unity and diversity

Figure 14. [2] micrometres. [2]

b. Estimate the magnic ation of the image. [2] c. Convert the dimensions from micrometres

to millimetres. Which length units are more

convenient with an organism of this size? [3]

s
s
e
r
P

y
▴ Figure 14 Ostrich egg

l
y
5. Caenorhabditis elegans has been widely used

n
▴ Figure 15 Caenorhabditis elegans together with an

as a model organism in research. Most adults are

eyepiece sc ale

t
hermaphrodite and have exactly 959 cells.

O
i
a. Measure the maximum width and total length of

s
the worm, in eyepiece units (EPU). [2]

b. One unit on the sc ale indic ates 9.5micrometres.

y
C alculate the actual dimensions of the worm in e

p
v

Quantitative versus qualitative observations

o
i

Quantitative data is numeric al and is usually obtained with 4. Discuss the advantages of qualitative and quantitative
n

a measuring instrument. An eyepiece sc ale (graticule) in observations.

a microscope is an example of a measuring instrument.

5. Do all quantitative observations involve a measuring

U

Sometimes quantitative data c an be obtained simply by

instrument? Or numbers? Or units?

n

counting. For example, we might count how many legs a

centipede has, to see if it is 100.

o

In contrast, qualitative observations involve descriptions

d

that are likely to be more subjective. Consider the

i

micrograph of pond water in Figure 16. An example of a

r

qualitative observation is that the copepod larva (centre

t
o

right) is transparent. Two types of algae are visible: Synura

a

appears yellow and Pandorina morum appears green.

f

1. Create a data table with two columns headed

x

“qualitative observations” and “quantitative

l

observations”.
O

2. M ake observations about the organisms in the

0.8 mm
micrograph and record them in your table.
v

▴ Figure 16 A micrograph of pond water

3. Compare your observations with those of a classmate.

E

56
 Cells

A2.2.3 Developments in microscopy

Microscopes were rst invented in the 17th century. Since then, there have been

many technological developments in microscopy, which have made new and

more detailed observations possible. Improved light microscopes in the second

s
half of the 19th century allowed the discovery of bacteria and other unicellular

organisms. Chromosomes were seen for the rst time and the processes of

s
mitosis, meiosis and gamete formation and fertilization were discovered. More

e
advanced microscopes also revealed the complexity of organs such as the kidney,

and the presence of mitochondria, chloroplasts and other structures in cells.

r
P
◂ Figure 17 Leeuwenhoek microscope of

y
about 1670 (le) and Zeiss microscope of

2020 (right)

l
y

n
t

O
i
s
r

y
e

p
30 point
v

o
i

20 point
n

At magnic ations of more than 400×, it becomes increasingly dicult to produce

10 point

a focused image with a light microscope. Imagine a pair of dots that appear
U

closer together as they become smaller. Eventually, it will be impossible to see

5 point
n

them as separate dots. A hand lens or microscope allows smaller details to be

distinguished but there is a limit bec ause of distortions c aused by the wavelength

4 point

of light.
o
d

This problem was overcome by the development of microscopes that use beams 3 point
i
r

of electrons instead of light. The wavelength of electrons is much shorter than

t

the wavelength of visible light. The rst electron microscopes were designed
2 point
o

and constructed in Germany during the 1930s. They c ame into use in research
a

laboratories in the 1940s and 50s. Some electron microscopes c an give

1 point
f

magnic ations up to 1,000,000×

u
x

▴ Figure 18 Size of printed periods (full

M aking the separate parts of an object distinguishable by eye is c alled resolution.
l

stops) used for punctuation c an be used to

Table 3 shows the maximum resolution of the unaided eye, the light microscope
O

test the resolution of the naked eye, and of

a

and the electron microscope, using three dierent SI size units.

the eye aided by one or more lenses. Font

size is the maximum height of letters and is

v

Resolution Resolution Resolution measured in “points”. In desktop publishing

millimetres / micrometres / nanometres / fonts, 1point is 0.353 mm. The diameter

E

of a period is just less than one-tenth of the

mm µm nm

overall font size, so a period at font size 30

Unaided eyes 0.1 100 100,000

has a diameter of approximately 1 mm. The

Light microscopes 0.0002 0.2 200

table shows a row of 10 periods at font sizes

from 30 to 1. Which sizes of period c an you

Electron microscopes 0.000 001 0.001 1

distinguish as individual dots?

▴ Table 3

57
 Unity and diversity

Bec ause electron microscopes have better resolution, they c an give much higher

magnic ation. This means much smaller structures c an be seen than with a light

microscope. Electron microscopes have allowed scientists to investigate the

detailed structure (ultrastructure) of cells. Variations in ultrastructure between

dierent cell types are described later.

s
Electron microscopes do have some disadvantages. They c an only give black

s
and white images, so any colour in electron micrographs has to be added

e
articially. The methods used to prepare material for the electron microscope

always kill the cells. In any c ase, cells would die inside an electron microscope

r
bec ause there is a vacuum and the beams of electrons are very destructive. In

contrast, light microscopes c an be used to examine living material and produce

y
images in colour. Therefore, both types of microscope are very useful in research

and continue to be widely used.

l
y
1. Fluorescent stains and immunouorescence

n
▴ Fig ure 19 An e l e c t ro n m i c ro sc o p e

in use at t he M a x-P l a nc k Ins t i t u t in H a l l e,

Most of the chemic als in cells are white or colourless so they are dicult to

t
Ge r m a ny. Th re e of t he m a ny t e c h no l o gi c a l

distinguish unless stained. Stains used in microscopy are coloured substances

O
d e ve l o p m e nt s in m i c ro s c o py a re

i
that bind to some chemic als but not others. For example, methylene blue binds

d e s c ri b e d he re

s
to DNA and RNA so it stains the nucleus dark blue and cytoplasm a lighter blue.

r
Fluorescence is when a substance absorbs light and then re-emits it at a longer

y
wavelength. Fluorescent stains have been used for over 100 years. Some absorb
e

p
ultraviolet light and re-emit it as blue light, for example. Special uorescence

fluorescent stain

microscopes have been designed and built with intense light sources such as
v

high power LEDs or lasers that emit a single wavelength. This light is absorbed

and re-emitted by the sample,

o
generating particularly bright images.
i
n

antibody Immunouorescence is a development of uorescent staining. Antibodies that

bind to particular chemic als (antigens) in the cell are produced. Then uorescent
U

markers of dierent colours are linked to these antibodies. A multicoloured

n

uorescent image c an then be produced showing where the chemic als are

antigen

loc ated. There are many research applic ations of this technique; for example, it

c an be used to nd out if one specic type of protein is being produced in a cell.
o
d

i
r

secondary
t

antibody
o

primary
f

antibody
x

l
O

fluorescent stain
v

antigen
E

▴ Figure 20 The uorescent stain (yellow)

may be linked directly to the antibody

that binds to the target antigen (green).

Alternatively, it may be linked indirectly by an

▴ Figure 21 In this image produced by immunouorescence, DNA in the nuclei is stained cyan.

antibody that binds to the primary antibody

Microtubule proteins of the cytoskeleton, which are normally invisible, are stained magenta. This

image was produced using a Nikon RTS2000MP custom laser scanning microscope

58
 Cells

2. Freeze-fracture electron microscopy

This technique is used to produce images of surfaces within cells. A sample is

plunged into liqueed propane at –190°C so it rapidly freezes. A steel blade is

then used to fracture the frozen sample. The fracture goes through the weakest

s
points of the cells. Some of the ice at the fractured surface is removed by

vaporization, to enhance the texture of the surface. This is c alled etching. Then a

s
vapour of platinum or c arbon is red onto the fracture surface at an angle of about

e
35° to form a coating. This creates a replic a of the fracture surface.

r
P

y
l
y

n
t

O
i
1. Cell is frozen 2. Cell is fractured 3. Cell is etched 4. Fractured surface is replic ated

s
▴ Figure 22 The freeze-fracture process

y
The replic a is removed from the frozen sample and c an be examined using an
e
electron microscope. It is about 2 nanometres thick on average but the thickness

p
varies bec ause of the angle at which the coating is applied. This gives the
v

impression of a 3D image through shadowing.

o
i

The weakest point in cells is usually the middle of membranes, between the two
n

layers of phospholipid. The freeze-fracture process gives a unique image of this

part of cells. When these images were rst produced, they led to a fundamental

change in theories about membrane structure. This is described in Topic B2.1

U

n
o
d

PM
i
r

t
o

OW
a
f

u
x

vacuole
l
O

cytoplasm
v
E

◂ Figure 23 Freeze-fracture image of a yeast cell, showing

LD

a large vacuole, smaller vesicles (unlabelled), plasma

membrane (PM), cell wall (CW) and a lipid droplet (LD). The

vacuole, vesicles and plasma membrane appear convex

or conc ave bec ause the fracture followed the centre of the

0.2 µm

membrane, which was curved. The lipid droplet is cross-

fractured bec ause it is not surrounded by a membrane

59
 Unity and diversity

3. Cryogenic electron microscopy

This technique is oen c alled cryo-EM. It is principally used for researching

the structure of proteins. A thin layer of a pure protein solution is applied to

a grid. The solution is ash-frozen, to create smooth vitreous ice and prevent

s
theformation of water crystals. Liquid ethane just above its melting point

of –182.6°C is usually used as the coolant.

s
Th e grid w i th the f roz e n p ro t e i n s o l u ti o n is pl a c e d in an e l e c t ro n m i c ro s c o p e

e
and d e t e c to rs re c o rd the p a tt e r n of e l e c t ro n s tra n s mi tt e d by i n di vi du a l

pro te i n molecules. Be c ause the pro t e i n mo l e c u l e s a re ra n d o m l y o r i e n ta te d

r
in th e l aye r of f roz e n s o l u ti o n , ma ny di ffe re n t pa tte r n s a re pro du c e d. Using

P
c o m pu ta ti o n a l algorithms, th e s e pa tt e r n s a re c o mb i n e d to pro du c e a 3D

y
i ma ge of th e pro t e i n molecules.

l
Previous methods for analysing protein structure only produced images of a

n
protein in its most stable form. However, cryo-EM analyses proteins at the instant

in time when the water around them froze. This allows scientists to research

O
proteins that change from one form to another as they c arry out their function.

i
s
Since 2010, cryo-EM techniques have improved rapidly. They c an now give

resolutions of 0.12nanometres. This allows the generation of images of individual

y
atoms in a protein or other molecule.
e O ver 10,000 protein structures have now

been shared in the Electron Microscopy D ata Bank (EMDB). The 2017 Nobel

p
Prize in Chemistry was awarded to Jacques Dubochet, Joachim Frank and Richard
v

Henderson for their work in developing cryo-EM. Figures 24 and 25 show an

o
example of this.
i
n

(a) (b) (c)

U

Pre
Post
n

ralloc
o
d

i
r

Tail
o

fibres
a

knurt
f

u
x

l
O

▸ Figure 24 Pyocin is a protein produced

by bacteria to kill other bacteria by bursting

v

their cell wall and membrane. The cryo-EM

image (a) shows pyocin pre-contraction

etalpesab
E

and post-contraction. The sc ale bar

represents 30 nm. Two computer-generated

coloured images of pyocin (b and c) show

components of the protein before and aer

spike

it contracts

60
 Cells

◂ Figure 25 This

collar
sequence of diagrams

shows how pyocin binds to

and then pierces its target

sheath

s
s
tail fibre

baseplate

e
outer membrane

r
cytoplasmic membrane
attachment contraction

y
inner tube

l
y

n
A2.2.4 Structures common to cells in all

t
living organisms

O
i
Cells vary considerably in size, shape and structure, but they share some

s
common features:

y
1. Plasma membrane e
This is the outer boundary of the cell and encloses all of its contents. The plasma

p
membrane controls the entry and exit of substances. It c an pump substances
v

in, even if the concentration outside the cell is very low. It is also very eective at

preventing entry of unwanted or even toxic substances. It allows a cell to maintain

o
i

concentrations of substances that are very dierent from those in the surrounding
n

environment. The permeability of the plasma membrane relies on a structure

based on lipids.
U

Occ asionally the plasma membrane of a cell bursts. This is known as lysis and
n

c an be c aused by excess pressure or by viruses. It c an even be c arried out by the

cell itself (autolysis). Lysis always leads to the death of the cell; this shows that the
o
d

plasma membrane is a vital structure.

i

2. Cytoplasm
r

Water is the main component of cytoplasm and there are many substances
o

dissolved or suspended in this water. Enzymes in the cytoplasm c atalyse

hundreds or even thousands of dierent chemic al reactions. These reactions are

f

the metabolism of the cell.

x

Metabolism provides a cell with energy and produces all the proteins and
l
O

other substances that make up the structure of a cell. Proteins are quite easily
a

damaged, so even when a cell is not growing the cytoplasm must continuously

break down and replace its proteins.

v

3. DNA
E

Genes, made of DNA, contain the information needed for a cell to c arry out all its

functions. M any genes hold the instructions for making a protein. Some proteins

are structural so are needed for growth and repair. Others act as enzymes,

without which a cell c annot control chemic al reactions and does not have a

functioning metabolism.

61
 Unity and diversity

DNA c an be copied and passed on to daughter cells, so the information it stores

is heritable. Plant and animal cells have a nucleus that contains almost all their

DNA. Bacteria do not have a nucleus and their DNA is in the cytoplasm instead.

Use of DNA as a genetic material is therefore common to all cells, but the loc ation

of this DNA is not universal.

s
s
A2.2.5 Prokaryote cell structure

e
Organisms c an be divided into two groups, prokaryotes and eukaryotes. Bacteria

r
are prokaryotic. Plants, animals, fungi and a variety of other organisms (such as

Amoeba) are eukaryotic. The key feature of eukaryotic cells is the nucleus, which

y
contains chromosomes. This is bounded by a nuclear envelope consisting of a

double layer of membrane. Prokaryotic cells do not have a nucleus.

l
y

n
Prokaryotes were the rst organisms to evolve on E arth and they still have

the simplest cell structure. They are mostly small in size and are found almost

t
everywhere—in soil, in water, on our skin, in our intestines and even in pools of

O
i
hot water in volc anic areas.

s
All cells have a plasma membrane. Some cells, including prokaryotic cells, also

r
have a cell wall outside the cell membrane. This structure is thicker and stronger

y
than the membrane. It protects the cell, maintains its shape and supports the
e

p
plasma membrane to prevent it from bursting. In prokaryotes, the cell wall

contains peptidoglyc an.

v

There is no nucleus in a prokaryotic cell

o
so the interior is entirely lled with
i

cytoplasm. The cytoplasm is not divided into compartments by membranes;

n

instead, it is one uninterrupted chamber. Prokaryotic cells are therefore

structurally simpler than eukaryotic cells—although they still contain a very

U

complex mixture of biochemic als including many enzymes.

n

The cytoplasm of eukaryotic cells contains organelles that are analogous to

the organs of multicellular organisms. Both organs and organelles are distinct
o
d

structures with specialized functions. Prokaryotes do not have cytoplasmic

organelles apart from ribosomes. Prokaryote ribosomes are smaller than those
i
r

of eukaryotes: they are 70S whereas eukaryote ribosomes are 80S. The S stands
t

for Svedberg units, which are a measure of the rate at which a particle sinks
o

during centrifugation.
a
f

In m a ny ele ctron m i c r o g ra p h s of prok aryotes, part of the cytoplasm a p p e a rs

u

lighter than the rest. This re gion contains DNA. There is usually only a
x

single molecule of DNA that forms a loop or c i rc l e. The DNA is “naked”:

l

unlike eukaryotic DNA, it is not a ss o c i a t e d with proteins. The lighter re gion

O

of the cytoplasm is c alled the nucleoid. It is similar to a nucleus bec ause

it contains DNA, but it is not a true nucleus. Other parts of the cytoplasm
v

appe ar darker in ele ctron m i c r o g ra p h s . They contain ribosomes, enzymes

and other proteins.

E

62
 Cells

Data-based questions: Ultrastructure of Clostridium

Figure 26 shows an electron micrograph of the Gram-

positive bacterium Clostridium botulinum. This bacterium nucleoid containing

cytoplasm with 70S

s
produces a neurotoxin that is the most poisonous protein naked DNA
ribosomes

so far discovered. This neurotoxin is used in cosmetic

s
0.5 μm
treatments under the brand name Botox®.

e
1. What c auses the cytoplasm of Clostridium to appear

so dark in the electron micrograph? [2]

r
2. This image is a longitudinal section: you c an see a thin

slice of the bacterium going from end to end. What

y
shape would you see in a transverse section (going

from side to side)? [1]

l
3. There are two nucleoids visible in the cytoplasm of this

n
cell. What does this suggest it is getting ready to do? [2]

t
4. There is a sc ale bar on the micrograph. Use this to

cell wall made

O
plasma membrane

c alculate the magnic ation of the micrograph. [3]

i
of peptidoglyc an
showing as a dark line

5. Use the magnic ation to c alculate the actual length

s
▴ Figure 26
of the cell. [2]

y
e

p
ATL Research skills: Using search engines eectively
v

Your task is to research the connection between c

o
Clostridium botulinum and cosmetic facial injections
i

Clostridium botulinum and cosmetic facial injections. What site:edu

n

cellular processes are aected?

Which search terms enabled you to answer the questions:

Your primary purpose is to use web-based sources to

“What is the connection between Clostridium botulinum
U

nd information. You should use precise language in your

and cosmetic facial injections?” and “What cellular
n

search terms, including scientic language. For example,

processes are aected by Clostridium botulinum?”

you might search “Clostridium botulinum” and “cosmetic

o

facial injections”. However, this is likely to return results

d

for businesses oering cosmetic treatments. These will be

sites with domain names ending in “.com”. For this task,

i
r

you want information from organizations whose primary

t
o

purpose is education. Such sites have domains ending

a

in “.edu”. To lter your search results, include the search

f

term “site: edu”.

u
x

Enter the following terms in your search engine. Compare

the results of the dierent searches.

l
O

a. Botox® treatment
a

b. Clostridium botulinum and cosmetic facial injections

▴ Figure 27 Injecting Botox®
v
E

63
 Unity and diversity

A2.2.6 Eukaryote cell structure

Eukaryotes, like all other living organisms, have a basic cell structure with

cytoplasm inside a plasma membrane. In some eukaryotes, there is also a cell

wall outside the membrane. Whereas the cytoplasm of a prokaryotic cell is one

s
undivided space, eukaryotic cells are compartmentalized. Areas are separated

from the rest of the cytoplasm by single or double membranes. The advantages

s
of having compartments are described in Topic B2.2. Three other fundamental

e
features distinguish eukaryotic cells from prokaryotic cells:

Nucleus

r
This compartment holds the cell’s chromosomes. The nucleus has a double

y
membrane with pores through it. E ach chromosome consists of one long

DNA molecule attached to proteins, except when a cell is preparing to divide

l
and the DNA is replic ated. The DNA molecules are linear rather than circular.

n
The proteins are histones, arranged in globular groups like small beads, with the

DNA wound around the outside.

O
i
80S ribosomes

s
Ribosomes in eukaryotic cells synthesize proteins, as in prokaryotes, but there are

structural dierences and they are larger in size. This c auses them to sink more

y
quickly than prokaryotic ribosomes when centrifuged; this is quantied using
e
Svedberg units (S). Eukaryotic ribosomes are 80S whereas those of a prokaryote

p
are 70S.
v

o
Mitochondria

▴ Figure 28 Whereas the DNA of

i

The cytoplasm of a eukaryotic cell contains mitochondria. A mitochondrion is

prokaryotes is naked, DNA in eukaryotes
n

surrounded by a double membrane. The inner membrane is usually folded inwards

is attached to groups of proteins c alled

histones. There are many of these histones to increase the surface area. Mitochondria carry out aerobic cell respiration, so in
U

along the chromosome, giving the overall eukaryotes they are only lacking in cells that never respire aerobically.

appearance of a string of beads

n

Nuclei, mitochondria and ribosomes are examples of organelles. All the

Source: C aputi, Francesca & C andeletti, S anzio &

Romualdi, Patrizia. (2017). Epigenetic Approaches

important organelles of eukaryotic cells are described in Section A2.2.10
o

in Neuroblastoma Disease Pathogenesis. 10.5772/

d

intechopen.69566

R
i
r

▸ Figure 29 An electron micrograph

o

of the unicellular fungus, Saccharomyces

a

cerevisiae (baker ’s yeast). The nucleus (N), m

f

mitochondria (m) and vacuole (V) are easily

u

visible. The cell wall (CW) is the thicker

x

pale outer layer. The plasma membrane

N
l

(PM) is the thinner dark line inside the cell

O

wall. 80S ribosomes (R) are smaller and

a

more dicult to see, but many are present.

V
m
The labelled ribosomes look like a string
v

of beads. This cell is 8 µm long. What is

m
the magnic ation of the micrograph?
E

Remember that 1 µm = 1,000 nm

PM
CW

64
 Cells

A2.2.7 Processes of life in unicellular

organisms

Living organisms are very diverse in their activities. However, some vital processes

are either universal or very widespread:

s
• homeostasis—maintenance of a constant internal environment in an organism

s
• metabolism—the sum of all the biochemic al reactions that occur in a

e
living organism

r
• nutrition—supplying the nutrients required for energy, growth and repair

in an organism

y
• excretion—removal of waste products of metabolism from an organism

l
• growth—an increase in size or number of cells

n
• response to stimuli—perception of stimuli and c arrying out appropriate

t
actions in response

O
i
• reproduction—production of offspring, either sexually or asexually.

s
In a multicellular organism, dierent cell types are specialized to perform these

r
functions, but the single cell of a unicellular organism must perform them all.

y
The annotated diagrams of Paramecium and Chlamydomonas (Figure 30 and
e

p
Figure 31) show how two unicellular organisms perform the functions of life.
▾ Figure 30 Paramecium
v

ood vacuoles contain smaller

Beating of whip-like cilia moves

o
organisms that the Paramecium has
i

Paramecium through the water.

consumed. These are gradually

This can be controlled by the cell

n

Metabolic reactions
digested and the nutrients are

so that it moves in a particular

take place in the
absorbed into the cytoplasm, where

direction in response to changes

cytoplasm, including
U

they provide energy and materials

in the environment.
the reactions that
n

needed for growth.

release energy by

respiration. Enzymes
o
d

in the cytoplasm

catalyse these
i
r

reactions.
t
o

a
f

u
x

l
O

a
v

The nucleus of the cell

E

can divide to produce

the etra nuclei needed

The contractile vacuoles at each end

when the cell reproduces. The cell membrane controls what

of the cell fill up with water and then

eproduction is often chemicals enter and leave. t

epel it through the plasma membrane

aseual, with the parent allows the entry of oygen for

of the cell. This is a type of homeostasis,

cell dividing to form two respiration. Ecretion happens

keeping the water content of the cell

daughter cells. by waste products diffusing

within tolerable limits.

out through the membrane.

65
 Unity and diversity

▸ Figure 31 Chlamydomonas
The cell wall is freely permeable.

The plasma membrane inside the Photosynthesis occurs

wall controls which chemicals inside the large cup-shaped

enter and leave the cell. For chloroplast. arbon dioxide

example, oxygen (a waste product is converted into compounds

s
of photosynthesis) is excreted needed for growth. ther

by outward diffusion through metabolic reactions happen

s
the plasma membrane. in the cytoplasm.

e
ontractile vacuoles

 store of starch

r
at the base of the

is visible inside

flagella fill up with

P
the chloroplast.

y
water and then expel

it through the plasma

l
Food vacuoles

membrane. This is a
Making c areful

n
are formed

type of homeostasis,

observations: when other

which eeps the water

t
organisms are
Examining a

O
content of the cell

i
ingested by

community of life within tolerable limits.

 μm endocytosis.

s
under a microscope

y
The two flagella beat to move the The nucleus of the cell can
To see unicellular organisms, follow
e
cell through the water.  light- divide to produce genetically
this procedure.

p
sensitive eyespot containing identical nuclei by asexual

1. Collect some pond water.

v

carotenoid pigments is visible reproduction. uclei can also

o
2. If possible, centrifuge the nearby. t allows the cell to sense fuse and then divide in a form
i

sample to concentrate the where the brightest light is and of sexual reproduction. n this

organisms in it. respond by swimming towards it. image, the nucleus is concealed
n

by the cup-shaped chloroplast.

3. Place a drop of the

U

concentrated pond water on a

microscope slide.
n

Data-based questions: Processes of life in a

4. Add a cover slip and view with

testate amoeba
o

a microscope.
d

Arcella gibbosa is a unicellular testate amoeba that lives in freshwater

You will almost certainly be able

i
r

habitats. It has a hard outer coat made of chitin, with a light but strong

to see unicellular organisms.

t

structure resembling honeycomb. This is c alled the test. There is a circular

o

Alternatively, you could obtain

a

aperture in the test and nger-like protrusions of cytoplasm c an push out

a pure culture of unicellular

through this, then retract again. In Figure 32, ve structures are labelled:
f

organisms such as Paramecium or

u

nuclear membrane (nm), outer surface of test (to), plasma membrane (pm),

Chlamydomonas
x

contractile vacuole (cv) and aperture in the test (at). The unlabelled coloured

structures are food vacuoles. A sc ale bar is shown lower right.

l
O

1. C alculate the diameter of the cell and the magnic ation of the
a

micrograph. [3]
v

2. Deduce the maximum size of food particle that could be ingested. [2]
E

3. Explain the need for a contractile vacuole in this organism. [3]

4. Predict whether this cell was:

a. growing [2]

b. preparing to divide. [2]

66
 Cells

5. Suggest a hypothesis for whether the cell has nm

to

mitochondria in its cytoplasm. Give reasons and

suggest how your hypothesis could be tested. [3]

s
pm

s
e
r
cv

y
l
at

n
t

O
i
s
50 μm

y
▸ Figure 32 Arcella gibbosa
e

p
v

A2.2.8 Dierences in eukaryotic cell

o
i

structure between animals, fungi and plants

n

Feature Animals Fungi Plants

U

Plastids None None Plastids of varied types

n

A family of organelles with two such as chloroplasts (for

outer membranes and internal photosynthesis) and

o

membrane sacs amyloplasts (to store starch)

d

Cell wall None Cells of fungi and plants have walls, composed
i
r

A rigid layer outside the plasma of chitin in fungi and cellulose in plants
t

membrane to strengthen and

o

protect the cell

f

Vacuole Small temporary vacuoles There is oen a large permanent vacuole in

u
x

A exible uid-lled compartment expel excess water or digest cells of fungi and plants, used for storage of

surrounded by a single membrane food or pathogens taken in by substances and pressurizing the cell
l

endocytosis
O

Centrioles Used to construct the spindle Absent, except in fungi and plants with
v

Cylindric al organelles that that moves chromosomes swimming male gametes, which have a centriole

organise the assembly of structures in mitosis and the 9+2 at the base of the agellum
E

composed of microtubules microtubules in cilia and agella

Undulipodia Cilia and agella are present in Absent except in fungi and plants with male

Cilia and agella used to generate many animal cells, including the gametes that swim using agella (tails)

movement of a cell or movement of tail of male gametes

uid adjacent to a cell

▴ Table 4

67
 Unity and diversity

ATL Thinking skills: Reecting on the reasonableness of results

It is claimed that, for every one of your human cells, there 3. Construct a model of a eukaryotic cell that is 10

are 10 prokaryotic cells living in your body. Does this seem times larger in every dimension: 100 mm × 50 mm ×

s
a reasonable claim? One way to test this claim is to model 50 mm.

it using artist’s clay.

4. Using these models, does the claim seem

s
1. Obtain some modelling clay.
reasonable?

e
2. Construct a model of a prokaryotic cell, with

dimensions 10 mm × 5 mm × 5 mm.

r
P

y
l
A2.2.9 Atypic al cell structure in eukaryotes

n
According to the cell theory, all living organisms are made of cells. E ach cell

t
is expected to have one nucleus (unless it is preparing to divide, when there

O
may be two). However, some structures in organisms do not follow the typic al

i
patterns. Some examples are red blood cells, phloem sieve tube elements,

s
skeletal muscle and aseptate fungal hyphae.

y
Red blood cells
e
In mammals, these cells do not have a nucleus. At a late stage in their

p
development in bone marrow, the nucleus is moved to the edge of the cytoplasm
v

and the small part of the cell containing it is pinched o and destroyed by a

phagocyte. Removal of the nucleus makes

o red blood cells smaller and more
i

exible, but they c annot repair themselves if they are damaged. For this reason,
n

they have a lifespan of only 100 to 120 days.

Phloem sieve tube elements

U

Plants move sap through tubular vessels, made from columns of cylindrical cells.

The ow of sap would be impeded if these cells had a typical structure. In xylem
o

vessels, which conduct watery sap from the roots to the leaves, all the dividing walls
d

between adjacent cells are removed and the plasma membrane and all of the cell

contents break down. This creates a hollow tube that no longer consists of cells.
i
r

In phloem, which conducts sugary sap from the leaves to other parts, the
o

conducting vessels are called sieve tubes. The dividing walls between adjacent

cells are sieve-like, with large pores for the sap to pass through. During
f

development of sieve tubes, the nucleus and most of the other cell contents
x

break down, but the plasma membrane remains as it is essential for phloem
l

transport. The subunits in a sieve tube are usually called elements rather than cells
O

because of their atypical structure. Sieve tube elements are connected to adjacent
a

companion cells, which have a nucleus and mitochondria. These companion cells
v

help the sieve tube elements to survive and carry out their function.

Skeletal muscle
E

▴ Figure 33 The human sartorius muscle

Some large multinucleate structures are formed when groups of cells fuse
c an be as much as 600 mm long. It contains

together. This type of structure is a syncytium. Muscle bres develop in this way.
muscle bres that extend from one end to

Columns of cells, each with a nucleus, are formed by cell division. These cells
the other. Are these the longest cells in the

human body? then fuse together to form long muscle bres.

68
 Cells

Aseptate fungal hyphae

In some growing cells, the nucleus divides repeatedly without any subsequent

cell division. This results in an unusually large multinucleate structure, known as a

coenocyte. The thread-like hyphae of some fungi develop in this way. Walls that

s
divide the hyphae of other types of fungi into uninucleate cells are c alled septa,

so hyphae without these divisions are aseptate.

s
e
r
P

y
l
y

n
t

O
i
s
r

y
e

p
v

▴ Figure 34 A micrograph of aseptate hyphae of the fungus Rhizopus

o
i

arrhizus, which is the most frequent c ause of mucormycosis. Spores

n

and the sporangia that produced them are also visible

U

A2.2.10 Cell types and cell structures viewed in light and

electron micrographs
o
d

In light micrographs, these features help us to identify whether a cell is from a prokaryote, a plant or an animal.
i
r

Prokaryotic cells Plant cells Animal cells

t
o

• single cells, sometimes arranged • always multicellular apart from • always multicellular apart from
a

in chains gametes and zygotes gametes, zygotes and blood cells

f

• small size—cells usually less than • larger size—cells usually more • larger size—cells usually more
u

5 µm than 5 µm than 5 µm
x

• oen rod-shaped (bacilli), • shape tends to be regular with • shape tends to be rounded with
l
O

spheroidal (cocci) or helic al at sides and cell junctions easily junctions between cells oen
a

(spirilli) visible in tissues hard to see in tissues

• cell wall present • cell wall present • no cell wall

v

• no nucleus; instead there is • nucleus normally present but not • nucleus normally present but not
E

a paler region of cytoplasm always visible always visible

(nucleoid)
• plastids present, such as • no chloroplasts or stored starch

• simple internal structure with no chloroplasts, or amyloplasts but cytoplasm contains many

membrane-bound organelles storing starch other organelles

• no vacuoles or other internal • large vacuole oen present • only small vacuoles are present

membranes

69
 Unity and diversity

Table 5 describes the structure and functions of all the main organelles of

eukaryotic cells.

▾ Table 5

Nucleus The nuclear membrane is double and has pores through

s
double nuclear it. The nucleus contains the chromosomes, consisting

membrane of DNA associated with histone proteins. Uncoiled

nuclear pores

s
chromosomes are spread through the nucleus in the

e
areas that appear pale and grainy. The small areas that

are more densely stained, mostly around the edge of

r
the nucleus, contain parts of chromsomes that have

remained coiled up (condensed). The nucleus is where

y
DNA is replic ated and transcribed to form mRNA, which
dense
chromatin

is exported via the nuclear pores to the cytoplasm.

chromatin

l
y

n
Rough endoplasmic The rER consists of attened membrane sacs, c alled

reticulum cisternae. Ribosomes are attached to the outside of

O
ribosomes these cisternae. They are larger than in prokaryotes and

i
are classied as 80S. The main function of the rER is to

s
synthesize protein for secretion from the cell. Protein

synthesized by the ribosomes of the rER passes into its

y
cisternae. It is then c arried by vesicles, which bud o and
e
are moved to the Golgi apparatus.

p
cisterna
v

o
Smooth endoplasmic Smooth endoplasmic reticulum consists of a branched
i

reticulum network of tubular membranes. In electron micrographs,

n

it appears as circles or ovals of membrane. The

membrane is smooth bec ause there are no ribosomes

U

attached. Smooth ER has a variety of functions. It is used

to synthesize lipids, phospholipids and steroids. A special

n

type of smooth ER stores c alcium ions in muscle when it is

relaxed.
o
d

Golgi apparatus This organelle consists of attened membrane sacs c alled

i
r

cisterna cisternae (as in rER). However, these cisternae are not as

t
o

long, are oen curved, do not have attached ribosomes

a

and have many vesicles nearby. The Golgi apparatus

f

processes proteins brought in vesicles from the rER. Most

u

of these proteins are then c arried in vesicles to the plasma

x

vesicles

membrane for secretion.

l
O

Lysosome These are approximately spheric al with a single

digestive enzymes membrane. They are formed from Golgi vesicles. They
v

contain high concentrations of protein, which makes

them densely staining in electron micrographs. They

E

contain digestive enzymes, which c an be used to break

down ingested food in vesicles. These enzymes c an also

break down organelles or even whole cells.

lysosome membrane

70
 Cells

A double membrane surrounds mitochondria. The

inner outer inner membrane is invaginated to form structures c alled

membrane membrane cristae. The uid inside is c alled the matrix. The shape of

mitochondria is variable but usually spheric al or ovoid.

They produce ATP for the cell by aerobic cell respiration.

s
F at is digested here if it is being used as an energy source

s
in the cell.

matrix

e
crista

r
Free ribosomes These appear as dark granules in the cytoplasm and are

not surrounded by a membrane. They have the same

y
size as ribosomes attached to the rER—about 20 nm in

diameter (known as 80S). Free ribosomes synthesize

l
protein, releasing it to work in the cytoplasm, as enzymes

n
or in other ways. Ribosomes are constructed in a region of

the nucleus c alled the nucleolus.

O
i
s
Chloroplast A double membrane surrounds the chloroplast. Inside

y
starch grain are
e stacks of thylakoids, which are attened sacs of

membrane. The shape of chloroplasts is variable but

p
usually spheric al or ovoid. They produce glucose
stroma
v

and a wide variety of other organic compounds

o
by photosynthesis. If chloroplasts have been
i

photosynthesizing rapidly, they may contain starch grains.

double
n

membrane
U

thylakoid
n

Vacuoles and vesicles These organelles consist of a single membrane with uid

vacuole inside. M any plant cells have large vacuoles that occupy
o
d

containing food more than half of the cell volume. Some animals absorb

foods from outside and digest them inside vacuoles.

i
r

Some unicellular organisms use vacuoles to expel

t

excess water.
o

Vesicles are very small vacuoles used to transport

materials inside the cell.

f

large vacuole
u

vesicles
x

Microtubules and centrioles The cytoplasm of cells contains small cylindric al bres
l

triple c alled microtubules. They have a variety of roles,

O

microtubules including moving chromosomes during cell division.

Animal cells h av e structures c alled centrioles, which

v

consist of two groups of nine triple mic rotubules.

Centrioles form an anchor point for mic rotubules

E

during cell division and also for mic rotubules inside

cilia and flagella.

71
 Unity and diversity

The cytoskeleton is constructed from several types of protein

bre. Tubulin is used to make microtubules and actin is

used to make microlaments. These structures can easily

be constructed or deconstructed, so the cytoskeleton is

dynamic. Microtubules guide the movement of components

s
within the cell. They help plant cells to construct cell walls.

s
A layer of microlaments just inside the plasma membrane

helps animal cells to maintain their shape.

e
Cilia and agella These are whip-like structures projecting from the cell

r
surface. They contain a ring of nine double microtubules

P
plus two central ones. Flagella are larger and usually only

y
one is present, as in a sperm. Cilia are smaller and many

are present. Cilia and agella c an be used for locomotion.

l
y
Cilia c an also be used to create a current in the uid next

n
to a cell.

t
double

O
plasma microtubule

i
membrane

s
r

y
e
A2.2.11 Drawing and annotation based on electron micrographs

p
v

Electron micrographs show cell structure in great detail. However, they sometimes include artefacts as well. (An artefact

o
is something that is not naturally present but was introduced as the specimen was prepared by staining and sectioning.)
i

Therefore, a drawing of an electron micrograph may show the structure more clearly. Basic drawing skills were described
n

earlier and Table 5 shows how the structure of organelles c an be shown in drawings.

Electron micrographs of a prokaryotic cell (Figure 35) and a eukaryotic cell (Figure 36) are shown. A drawing of the
U

prokaryotic cell is also included, to show how its structure c an be interpreted. Organelles in the electron micrograph of

a eukaryotic cell are labelled. Using your knowledge of these organelles, you should be able to draw the whole cell to
n

show its ultrastructure.

o
d

i
r

t
o

a
f

nucleoid
x

(region containing
l

ribosomes cell wall plasma membrane cytoplasm naked DNA)

O

a
v
E

▴ Figure 35 Electron micrograph of Escherichia coli (1–2 µm in length), with a drawing to

help interpret the micrograph

72
 Cells

free

mitochondrion nucleus ribosomes

s
s
e
r
P

y
l
y

n
t

O
i
s
r

y
e

p
v

rough endoplasmic Golgi lysosome

o
reticulum apparatus
i

▴ Figure 36 Electron micrograph of a liver cell. The plasma membrane is visible as a dark line. Part of the cell on the
n

right is not visible

U

LHA
A2.2.12 Origin of eukaryotic cells by

endosymbiosis
o
d

Symbiosis is living together in a close association. In endosymbiosis, one

i
r

organism (the endosymbiont) lives inside another (the host). In the closest form
t

of this, the endosymbiont lives inside a cell of the host. The endosymbiont enters
o

the host cell by endocytosis. This is the process that cells use to make a vesicle
a

or small vacuole by pinching o a piece of the plasma membrane. It is described

f

fully in Topic B2.1

x

Cells c an use endocytosis to ingest other, smaller cells. For example, phagocytes
l

in humans ingest viruses or bacteria, and unicellular organisms such as

O

Paramecium ingest the organisms on which they feed. In those c ases, digestive

enzymes are added to the vacuole to break down the ingested organisms,
v

which are therefore killed. In other c ases, the host c an gain more from the

ingested organism if it is alive. The result is endosymbiosis. In a mutualistic

E

relationship, both the host and the endosymbiont benet. Examples of mutualisic

endosymbiosis are studied in Topic C4.1

Endosymbiosis almost certainly contributed to the evolution of eukaryotic

cells. According to a well-established theory, mitochondria were once free-

living prokaryotes that developed the process of aerobic respiration. L arger

prokaryotes that could only respire anaerobic ally took in these smaller

73
 Unity and diversity
LHA

prokaryotes by endocytosis; instead of killing and digesting them, they allowed

the engulfed cells to live in the cytoplasm as endosymbionts. Aerobic respiration

in the endosymbiont supplied energy to the host, far more eciently than the

host’s own anaerobic respiration. At the same time, the endosymbiont was

supplied with food by the host. Natural selection therefore favoured cells that

s
developed this mutualistic endosymbiotic relationship.

s
If the endosymbionts grew and divided as fast as the host cell, they could persist

e
inside host cells for many generations. According to the endosymbiotic theory, we

can deduce that they have persisted inside eukaryotic cells for hundreds of millions

r
of years, evolving to become the mitochondria of eukaryotic cells alive today.

y
l
y

n
t

O
i
s
embrane invagination
Shared features Outgrowths of the plasma The aerobic eubacterium

r
and vesicle formation

y
suggest that membrane expanded the became totally enclosed by

generated organelles which

eukaryotic cells cytoplasm. The archaean endosymbiosis and developed
e

p
became more complex and
evolved from DA remained in the into the mitochondrion. n

diverse. An association
v

the cells of an centre and the membrane some cells, a cyanobacterium

developed with an

o
archaean, around it started to develop also became enclosed and

aerobically respiring
i

usually known into the inner nuclear developed into chloroplasts.

eubacterium.
as Asgard. membrane.
n

▴ Figure 37 Origins of the nucleus, mitochondria and chloroplasts

U

The endosymbiotic theory also explains the origin of chloroplasts. If a prokaryote

that had developed photosynthesis was taken in by a host cell and allowed
o
d

to survive, grow and divide, it could have developed into the chloroplasts of

photosynthetic eukaryotes—algae and plants. Again, both the endosymbiont and

i

the host would benet from the relationship.

r

t
o

This explanation for the evolution of mitochondria and chloroplasts remains a

a

theory bec ause it c annot be conclusively proved. However, the features of both

mitochondria and chloroplasts provide strong evidence for it:

f

u
x

• They have a double membrane. This would be expected if a prokaryote with

a single plasma membrane was ingested by endocytosis.

l
O

• They have their own genes, on a circular DNA molecule like that of
a

prokaryotes.
v

• They transcribe their own DNA and use the mRNA to synthesize some of their

own proteins.
E

• The ribosomes they use for protein synthesis have a size (70S) and structure

more typic al of prokaryotic cells than eukaryotic.

• They c an only be produced by division of pre-existing mitochondria and

chloroplasts.

74
 Cells

LHA
Eukaryotes

Bacteria Archaea

s
s
e
r
P

y
l
y

n
LUCA

O
i
s
▴ Figure 38 Evidence suggests that the mitochondrion was originally a member

y
of the domain Bacteria and the host cell that took it in was a member of the domain
e
Archaea. In the tree of life, the domain Eukaryota was therefore formed by uniting

p
two branches rather than by splitting o a branch
v

o
i

Theories: The theory of endosymbiosis

n

Use the theory of endosymbiosis to make predictions:

U

1. Mitochondria have a double membrane. Predict

n

which membrane would have prokaryotic features

and which would have eukaryotic features.

o
d

2. There are ribosomes within the matrix of

mitochondria. Predict whether the ribosomes within

i
r

mitochondria are 70S (like those of prokaryotes) or

t

80S (as in eukaryotes).

o

Use the theory of endosymbiosis to explain these features:

f

1. Mitochondria and chloroplasts have circular DNA,

u
x

rather than linear DNA with two ends.

l

2. Human mitochondrial DNA has only 16,569 base ▴ Figure 39 Inside this protozoan (Paramecium bursaria),
O

there are individual cells of a green alga. The two organisms

pairs, compared with an average of 143,000,000
a

have a mutualistic relationship. The algae photosynthesize

base pairs of human chromosomes loc ated in the

inside the Paramecium, providing it with sugars and oxygen,

v

nucleus.

while deriving protection and c arbon dioxide from their host.

3. There are only 37 genes in human mitochondrial

In what way does this support the theory of endosymbiosis?
E

DNA, compared with more than 500 in free-living

prokaryotic cells.

75
 Unity and diversity
LHA

A2.2.13 Cell dierentiation as the

process for developing specialized

tissues in multicellular organisms

s
Multicellular organisms have an advantage bec ause cells c an develop

dierently to perform dierent functions. Specialized cells develop only

s
the features they need to c arry out their functions, which makes them more

e
ecient. For example, red blood cells transport oxygen using the protein

haemoglobin. They produce large amounts of this protein but do not

r
produce other proteins that they would not use.

y
Some activities are needed in all cells, such as release of energy by

respiration. About 4,000 genes have been detected in human cells that are

l
active in all cell types. They are c alled housekeepeing genes and they are

n
not associated with specialized roles. Other genes vary in their expression

and in some c ases are only ever active in a single cell type.

O
The development of specialized cell types happens from a very early stage

i
in the life of humans and other organisms. Even in a tiny embryo, dierent

s
cells begin to take dierent pathways of development. This is the process

r
of cell dierentiation. In dierentiated cells, dierent genes are “switched

y
on” and expressed, so the cell makes particular proteins and other gene

▴
e
Figure 40 Biologists recently analysed

products. The control of which genes act in a cell is c alled gene expression.

p
600,000 dierent cells from all parts of the human
v

body to nd out which genes they were using.

A total of 102 cell clusters were discovered,

corresponding to dierent tissues or organs of the

A2.2.14 Evolution of multicellularity
o
i

body. E ach of these clusters contained dierent

n

All plants and animals are multicellular. Multicellularity has evolved

cell types. For example, 17 distinct cell types

independently more than once in the origins of plants and at least once

were found in the liver cluster. This image shows

in animals. M any fungi and eukaryotic algae are multicellular. Even some
U

similarities in gene use between individual liver

prokaryotes cooperate to form multicellular aggregates. Most cells within a

cells as a two-dimensional distribution

n

multicellular organism have lost the ability to live independently or to divide.

o
d

all multicellular

some multicellular, some unicellular

i
r

mostly unicellular, some multicellular

t

all unicellular or colonial

o

plants mostly unicellular, rarely colonial

a

all unicellular
f

charophycean algae
x

rhizaria
red algae

chlorophycean algae
l

dinoflagellates
O

prasinophytes

ciliates
v

lobose amoebas diatoms

E

dictyostelid slime other

moulds stramenopiles

plasmodial slime excavates,

▸ Figure 41 This evolutionary tree

moulds e.g. Euglena

diagram shows all the major groups of

eukaryotes and shows that multicellularity fungi

choanoflagellates

evolved separately in dierent groups acrasid

slime moulds
animals

76
 Cells

LHA
There are several advantages to multicellularity. Multicellular organisms tend

to have longer lifespans, bec ause the death of one cell does not prevent the

continued survival of the individual. Multicellular organisms are generally

larger than unicellular organisms, so they c an exploit niches that single-celled

organisms c annot. Multicellularity also allows for complexity as there c an be

s
dierentiation of cell types within an organism.

s
Nonetheless, most of the individual living organisms on E arth are single-celled

e
and most of the biomass on E arth consists of single-celled organisms. This

suggests that although some traits possessed by multicellular organisms (such as

r
longer lifespans and dierentiation) are advantages, unicellular organisms must

have a relative advantage in some situations.

y
l
y

n
t

O
i
s
r

y
e

p
v

o
i
n

C
U

n
o
d

▴ Figure 42 Myxococcus xanthus is a rod-shaped Gram-negative bacterium ▴ Figure 43 A slime mould c an exist as a number of

that lives in the soil and feeds on other species of bacteria. It is found in slow-moving single-celled protists, each of which engulfs
i
r

clusters, c alled swarms, which act as a collective unit and show coordinated solid food particles. Under certain conditions, the single
t
o

movement in response to environmental cues. The bacteria are also able to cells group together to form a multicellular body c alled
a

dierentiate to form multicellular inactive (resting) spores that are resistant to the plasmodium. This c an then form into a reproductive

drying out. They form when the availability of nutrients is limited. They have spore tower. Most slime moulds are saprophytes,
f

the adaptive advantage that when conditions become more favourable, the feeding on dead or dec aying organic matter
x

cells will reactivate as a swarm

l
O

a
v
E

77
 Unity and diversity
LHA

Data-based questions: Diversity in green algae

1. a. State the shape of the cells in the two species

of algae. [2]

s
b. Most of the cells of K. klebsii have only one

chloroplast. Describe the features of these

s
chloroplasts that can be seen in the micrograph. [3]

e
c. Explain a reason for the hypothesis that some

K. klebsii cells must contain two chloroplasts. [1]

r
d. Spherical lipid droplets are visible in the cytoplasm

P
of both species, but nuclei are not visible. Outline
▴ Figure 44 Two species of green algae, with

y
how the nuclei could be made visible. [1]
Klebsormidium klebsii above and Crucigenia fenestrata below

e. Discuss whether K. klebsii and C. fenestrata

l
y
are unicellular or multicellular. [3]

n
2. Staurodesmus convergens is a desmid. These algae

t
have two symmetric al parts to their cells, linked by

O
i
a bridge where the nucleus is loc ated. E ach of the

two “semi-cells” contains one large chloroplast with

s
a circular store of starch. There are two layers in the

r
cellulose cell wall. In the outer layer the cellulose is

y
impregnated with other substances and oen forms
e

p
spines or other protrusions.
v

a. C alculate the maximum length of the cell,

o
with and without the spines. [2]
i

b. Suggest a function for the spines. [2]

n

c. This alga secretes a mucus coat outside its cell

25 μm
wall. Cylindric al bacteria, which are always
U

present, are visible in this mucus. C alculate

n

the length of one of these bacteria. [1]

▴ Figure 45 Staurodesmus convergens

d. Suggest benets of the mucus to the bacterium,

o
d

and also to the alga. [3]

i
r

e. Discuss whether this alga is one cell or two. [2]

t

3. The alga on the le is the desmid Bambusina

o

brebissonii and the alga on the right is the desmid

Staurastrum senarium. Between them is a ciliated

f

protozoan that has engulfed cells of the alga Chlorella

x

by endocytosis.
l

a. Identify three similarities and two dierences

O

between the cells of B. brebissonii and

S.senarium that are visible in the micrograph. [5]

v

b. The cilated protozoan has engulfed more than

E

15 Chlorella cells. C alculate the diameter of the

25 μm

largest of these Chlorella cells. [2]

c. Discuss the relative advantages to the ciliated

▴ Figure 46 Bambusina brebissonii (le),

protozoan of digesting or not digesting the

Staurastrum senarium (right) and a ciliated

Chlorella cells. [4] protozoan (centre)

78
 Cells

Linking questions

1. What explains the use of certain molecular building blocks in all living

cells?

s
a. Outline the diverse roles of proteins in living cells. (B1.2.12)

s
b. Explain how hydrophobicity contributes to compartmentalization in

cells. (A2.1.5)

e
c. Describe the diverse forms that the genetic material takes in cells.

r
(A2.2.10)

y
2. What are the features of a compelling theory?

a. A new multicellular plant is discovered. Predict the features that

l
would be observed in the cells of the organism.

n
b. Using the theory of endosymbiosis and the theory of evolution by

t
natural selection, explain the evolution of:

O
i
i. eukaryotic cells (A2.2.12)

s
ii. multicellularity. (A2.2.14, A4.1.1)

y
c. Using one theory, such as the theory of endosymbiosis or
e the theory

of evolution by natural selection, discuss the extent to which the

p
theory is useful for:
v

i. explaining observations (A4.1.1, A2.2.12)

o
i

ii. predicting observations. (A4.1.1, A2.2.12)

n

C
U

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

79
 A2.3 Viruses
LHA

How c an viruses exist with so few genes?

s
s
Figure 1 shows a human cell infected with inuenza (u) virus. Viruses vary in

the total number of genes they have. For example, the inuenza virus has just

e
8 genes while the human HHV-6 virus (Figure 2) has more than 100genes.

What is the minimum number of genes found in any cell? How does this

r
compare to the virus with the largest number of genes? How can viruses

y
endure with so few genes? In what ways are viruses dependent on their

hosts? Are there any types of genes which are found in all viruses? Do RNA

l
viruses have genes?

n
t

O
i
s
r

y
▴ Figure 1 The micrograph shows a human cell
e
infected with inuenza (u)virus

p
v

In what ways do viruses vary?

o
i
n

The herpes viruses shown in Figure 2 are about to be taken up by a

white blood cell which will become their host. This virus, HHV-6, infects
U

nearly all humans in early childhood resulting in a variety of symptoms

n

including a rash c alled roseola. The virus is also taken up by white blood

cells c alled T-lymphocytes and B-lymphocytes. What generalizations c an

o
d

be made about all viruses? What are some of the ways that viruses show

structural variability? What is the dierence between the lytic cycle and the
i

lysogeniccycle?
r

t
o

a
f

u
x

l
O

▴ Figure 2 Herpes viruses about to be taken

up by a white blood cell

v

AHL only
E

A2.3.1 Structural features common to viruses

A2.3.2 Diversity of structure in viruses

A2.3.3 Lytic cycle of a virus

A2.3.4 Lysogenic cycle of a virus

A2.3.5 Evidence for several origins of viruses from other organisms

A2.3.6 R apid evolution in viruses

80
 Cells

LHA
A2.3.1 Structural features common to viruses

Viruses are non-cellular agents that infect cells and reproduce inside them. Unlike

living organisms, which share common features bec ause they are all descended

nanometre
nm =
from a single common ancestor (LUCA), viruses probably have multiple origins,

1000 pm
1 nm =

s
as they share relatively few features. Features that they do have in common are
picometre
pm =

examples of convergent evolution—they developed for functional reasons: 1000 fm

1 pm =

s
femtometre
fm =

• Small size—Most viruses are between 20 and 300 nanometres in diameter. This

e
is smaller than almost all bacteria and much smaller than plant or animal cells. –7
10

Viruses must be smaller than their host cells so they can enter them. Viruses are

r
smallest viruses

also small because they lack cytoplasm and other structural features. diameter = 20 nm

–8
10

y
• Fixed size—Viruses do not grow so they do not increase in size. A virus is
DNA molecule

assembled inside a host cell, in a similar way to a c ar being assembled from diameter = 2 nm

l
–9
10
components—both a virus and a c ar are their full size as soon as assembly is

n
completed. M any viruses are composed of a fixed number of components,

hydrogen atom
each with a fixed size, so this determines the overall size.
–10

t
10
diameter = 100 pm

O
• Nucleic acid as genetic material—All viruses have genes made of DNA

i
or RNA and they use the universal genetic code. This is essential as their
–11

s
10

proteins are synthesized by the nucleic acid-to-polypeptide translation

r
mechanisms of their host cell.

y
–12
10

• C apsid made of protein—Before viruses are released from their host cell,
e

p
their genetic material is enclosed in a protein coat c alled the c apsid. This
v

–1
is made of repeating protein subunits. A few viruses have only one type of
10

o
protein in the c apsid, but most have several. Self-assembly of the repeating
i

subunits of the c apsid gives viruses a symmetric al structure that is strikingly

–1
10
n

different from the shape of living cells.

proton

• Viruses released from host cells have no cytoplasm and contain no (or very
diameter = 2 fm

–1
U

10
few) enzymes. Even when a virus has infected a host cell, relatively few viral
n

enzymes are produced bec ause viruses rely on the metabolism of the host.

▴ Figure 3 This logarithmic sc ale shows

The viral enzymes that are produced are required for replic ation of the virus’s

the relative size of viruses

genetic material, for infecting host cells or for bursting host cells to release
o
d

the new viruses.

i
r

t
o

a
f

u
x

l
O

a
v

◂ Figure 4 Cryo-electron microscope images

of mimivirus, an exceptionally large virus, that

E

uses Amoeba as its host. Colouring indic ates

distances from the centre of the virus. The grey

area (0 – 180 nm from the centre) holds double

stranded DNA that is the genetic material of the

virus. The rainbow colouring (red to blue =180

to 250 nm) shows the c apsid. A distinctive

feature of this virus is the starsh shaped vertex

on the surface of the c apsid

81
 Unity and diversity
LHA

A2.3.2 Diversity of structure in viruses

Viruses are very diverse in shape and structure. No genes occur in all viruses.

Based on this observation, scientists have deduced that viruses have multiple

evolutionary origins.

s
1. Diversity of genetic material

s
Viruses have genes made of either DNA or RNA. When a virus enters a

host cell, the DNA or RNA could be single or double stranded. There is

e
considerable variation in length of the nucleic acid molecule and it may be

circular with no ends or linear with two ends. There is further variation in how

r
viruses replic ate their genetic material and use it during protein synthesis. For

P
example, single-stranded RNA viruses use one of three dierent methods:

y
• positive-sense RNA viruses use their genes directly as messenger RNA

l
• negative-sense RNA viruses transcribe their genes to make messenger

n
RNA

t
• retroviruses make double-stranded DNA copies of their RNA genes and

O
i
then transcribe the negative-sense strand of the DNA to produce mRNA.

s
2. Enveloped and non-enveloped viruses

To be released from their host cell, viruses burst it in a process c alled lysis.

y
Some viruses become covered in a membrane during this process. This is
e
particularly common in viruses that infect animal cells. The phospholipids in

p
the membrane around the virus are derived from the plasma membrane of
v

the host cell. The proteins, mostly glycoproteins, come from the virus itself.

o
The membrane helps the enveloped virus to make contact with a host cell
i

and infect it.

n

Other viruses do not become enclosed in a membrane. They are c alled non-

enveloped viruses. Most viruses that infect bacteria or plant cells are non-
U

enveloped. Table 1 summarizes some key properties of three dierent viruses.

n
o

A2.3.3 Lytic cycle of a virus

d

Bacteriophage lambda has proteins at the tips of its tails which bind to the outer
i
r

surface of its host, Escherichia coli (E. coli). The DNA of this virus enters the host
t

cell through its tubular tail. The viral DNA has single-stranded ends, which link
o

by base pairing to convert the molecule from a linear to a circular form. Two

alternative strategies c an then be followed:

f

u
x

• Lysogenic cycle—The viral DNA becomes integrated into the bacterial DNA

mammals
molecule, so new whole virus particles are not produced. This is described in
l
O

Section A2.3.4.
a

birds and reptiles

• Lytic cycle—The virus reproduces and then bursts out of the host cell, killing
v

it. This is illustrated in Figure 6.

amphibians
E

Bacteriophage lambda is virulent when it follows the lytic cycle bec ause it

▴ Figure 5 A cladogram showing

destroys its host. It c an spread to more and more E. coli bacteria but as it kills

relationships between coronaviruses, based

them it must continue to nd new host cells. If lambda or other bacteriophages
on base sequences of their RNA genomes.

kill an entire population of bacteria, they are at risk of dying out themselves.
Dierent colours indic ate the class of the

host. How easy is it for a virus to change to a

Viruses that infect cells in plants or animals oen follow a lytic cycle. As a result,

dierent class of host?

they spread from cell to cell within the host organism. The viral infection becomes

Source: Shi, M. et al. Nature 556, 197–202 (2018).

82
 Cells

LHA
increasingly widespread within the body and the eects of the disease become

more severe. Usually, an animal host will be able to ght o viruses multiplying by

the lytic cycle. For example, humans produce antibodies that destroy all copies

of a virus within the body. If a viral infection remains uncontrolled, however, it c an

become life-threatening for a multicellular host.

s
Virulence therefore has disadvantages for a virus. The virus may be detected and

s
destroyed by the host, or it may lose its host by killing it. In either c ase, the virus

e
c an only persist if it spreads to another host.

r
Bacteriophage lambda COVID-19 HIV

y
Type of Bacteriophage (a DNA virus that Coronavirus (an RNA virus with Retrovirus (a virus that converts

l
virus uses either a bacterium or an a crown-like shape that uses an its RNA genome to DNA aer

y
archaean as its host) animal cell as its host) infecting a host)

n
t
Enveloped Non-enveloped Enveloped Enveloped

O
or non-

i
enveloped

s
r
Genetic One double-stranded DNA One single-stranded positive- Two copies of a single-stranded

y
material molecule with positive and sense RNA molecule with 29,903 positive-sense RNA molecule of
e
negative sense strands and bases. 9,749 bases.

p
48,502 base pairs. The 16 genes code for 29 There are 9 genes, coding for
v

There are 32 genes which code for proteins, including 4 structural 15 viral proteins, including 4

29 proteins including 4 enzymes. proteins and 6 enzymes.

o enzymes.
i
n

Distinctive The virus c an follow either a lytic COVID-19 c aused a pandemic, The virus contains the enzyme

features cycle (in which it reproduces and starting in 2020. It is an example reverse transcriptase which makes
U

then kills the host cell as it bursts of a zoonosis, bec ause it was a double-stranded DNA copy
n

out) or a lysogenic cycle (in which passed to humans from another of the viral RNA genome. This is

it integrates its DNA and does not species, probably a bat. then integrated into a host cell

kill the host). chromosome.

o
d

Host Escherichia coli— Human cells and possibly cells in T-helper cells in the human
i
r

a Gram-negative bacterium other mammals immune system

t
o

a
f

u
x

l
O

matrix protein
membrane RNA packaged

envelope with globular

v

proteins
with three types proteins

embedded in
of protein protein

the membrane
E

embedded in it coat

(capsid)

spike proteins

that bind to

reverse

host cells

transcriptase

lipid

bilayer

envelope

▴ Table 1

RNA associated with globular proteins

83
 Unity and diversity
LHA

1 Attachment

Proteins in the tip of the tail bind to maltoporin, a

protein in the outer membrane of E. coli used for

absorption of carbohydrates.

2 DNA entry

s
The viral DNA molecule enters the host

via the pore in maltoporin and another

s
pore protein in the inner membrane of

e
the bacterium.

r
P

y
l
y

n
t

O
i
s
r

y
e

p
7 Spread 3 DNA replication
v

The cell contents burst out, The ends of the linear viral DNA

o
toether ith about molecule join up to form a circle.

The lytic cycle

i

100 viruses. The viruses The viral DNA is replicated

can spread to infect other

n

around 100 times by a

C

host cells. "rollin circle" method.

U

n
o
d

i
r

t
o

a
f

u
x

6 Lysis 4 DNA transcription

l
O

iral proteins mae holes essener NA copies of viral enes

a

throuh the all and membranes are made. These are then translated

of the host cell. to mae viral proteins.

v
E

5 Protein synthesis

iral proteins are synthesied usin host cell ribosomes. nitially,

proteins are made for use durin DNA replication and other functions

hile the virus is inside the host. Then lare uantities of head and tail

proteins are made. These selfassemble to form capsids, ith one copy

of the viral DNA molecule inside each capsid.

▴ Figure 6 The lytic cycle

84
 Cells

LHA
A2.3.4 Lysogenic cycle of a virus

The lysogenic cycle, shown in Figure 7, is an alternative to the lytic cycle.

s
The lysogenic cycle 4 Cell division

When the bacterial host replicates its DNA,

s
prior to cell division, it also replicates the

prophage. Both of the daughter cells

e
contain the prophage.

1 Attachment

r
roteins in the tip of the tail bind to maltoporin,

P
a protein in the outer membrane of E. coli used

y
for absorption of carbohydrates.

l
y

n
t

O
2 DNA entry

i
The

The viral DNA molecule enters the host via

s
lysogenic

the pore in maltoporin and another pore

cycle

protein in the inner membrane of the

y
bacterium.
e

p
v

3 Integration

The viral DNA becomes circular. Then it is

o
i

inserted into one specific position in the

n

bacterial DNA by the viral enzyme integrase.

Aer this, the virus only eists as a length

U

of DNA called the prophage.

n
o
d

▴ Figure 7 The lysogenic cycle

i
r

t
o

While a virus remains in the lysogenic cycle, it is “temperate”: it does not kill its
a

host and it c auses minimal harm. The virus remains undetectable as a prophage in
f

the bacterial DNA. It is inherited by daughter cells but c annot spread by infecting
u

uninfected cells.
x

A temperate virus existing as a prophage is c alled “lysogenic” bec ause it could

l
O

change to the lytic state and then c ause lysis. For this to happen, genes in the
a

prophage must be activated in response to stimuli from inside or outside the

bacterial cell.
v

Temperate viruses c an benet the host cell bec ause their DNA may include
E

genes transferred from a previous host. These genes become integrated into the

bacterial DNA along with the viral genes. This increases the genetic diversity of

the bacterial host, facilitating evolution.

85
 Unity and diversity
LHA

ATL Justifying hypotheses:

Data-based questions: M arine viruses

C auses of the switch

Water samples were taken from the St Petersburg city pier in Tampa, Florida

to the lytic cycle in

every two weeks for 13 months. The numbers of bacteria and viruses in the

s
samples were counted. The concentrations of chlorophyll a were measured
Herpes simplex viruses

to give an estimate of the abundance of photosynthetic algae. Temperature

s
and salinity of the water samples were also measured. Table 2 shows
In everyday language, a

e
correlation coecients between these variables. In the area where samples
hypothesis is oen referred to as

were taken, there is most rainfall in summer.

an “educ ated guess”. This means

r
there is a reasonable theoretic al

Numbers

justic ation for the hypothesis.

y
of viruses

Once a hypothesis is generated, it

Numbers of Numbers
is worded as a testable statement

0.561

l
bacteria of bacteria
that c an be investigated through

n
an experiment. A well-worded
Chlorophyll a Chlorophyll a

0.725 0.513

hypothesis will suggest the method

concentration concentration

O
that should be followed to test it.

Temperature 0.649 0.793 0.588 Temperature

i
S alinity −0.803 −0.518 −0.750 −0.534

s
Source: Jiang and Paul. 1994. M arine Ecology Progress Series. Vol. 104. Pp 163–172.

y
▴ Table 2
e
1. Explain what is indic ated by a correlation coecient of 1.00. [1]

p
v

2. Some of the correlation coecients are positive and some are negative.

o
Explain what is indic ated by:
i

a. a positive correlation coecient [1]

▴ Figure 8 A cold sore
n

Cold sores are caused by one b. a negative correlation coecient. [1]

variant of the Herpes simplex virus,

7 7 3
U

3. Numbers of viruses varied between 0.22 × 10 and 3.0 × 10 per cm .

known as HSV1. This virus alternates

n

Suggest a reason for the correlations between the numbers of viruses

between a dormant lysogenic phase

and:

and an active lytic phase; during the

o
d

a. numbers of bacteria [1]

lytic phase, it causes painful blisters.

Aected individuals oen spend a

b. chlorophyll a concentration [1]
i
r

period of time symptom free. What

c. salinity. [1]
t

causes the virus to convert to the

o

lytic cycle?
4. Discuss the diculties of analysing correlation coecients. [2]
a

Hypothesis 1: If the host is in poor

f

5. Bacteria from the samples were tested to nd out whether they
u

health, then the virus will convert to

contained prophages. Four out of ten bacteria tested positive.

x

the lytic cycle.

C alculate the percentage occurrence of lysogeny in bacteria in

Hypothesis 2: If the host is in

l

seawater at St Petersburg city pier. [1]

O

robust health, then the virus will

a

convert to the lytic cycle.

v

While viruses are not living, they are

A2.3.5 Evidence for several origins of

subject to selection pressures and
E

the most t adaptations encoded

viruses from other organisms

in the viral DNA will determine

Viruses are simpler in structure than cells, suggesting the hypothesis that they

successful reproduction. Use the

evolved rst. All viruses use the same genetic code, with a few insignic ant

theory of natural selection to justify

dierences. If they did evolve before cells, the universality of the genetic code

both of these hypotheses.

implies a single ancestral virus with this code, from which all existing viruses

86
 Cells

LHA
are descended. However, the diversity in structure and genetic constitution of

viruses (described in Section A2.3.2) suggests multiple origins rather than a single

common ancestor.

Viruses are obligate parasites. They need a host cell in which to replic ate. An

s
obvious deduction is that cells must have evolved before viruses. All living

organisms use essentially the same genetic code, inherited from LUCA. Viruses

s
also use this code. It seems reasonable to deduce that viruses must have evolved

e
from cells. There are two types of hypothesis for the mechanism of evolution.

1. Progressive hypotheses

r
Viruses are built up in a series of steps by taking and modifying cell

components. This ts with the observation that there are virus-like

y
components in some cells, for example retrotransposons.

l
Retrotransposons are sequences of nucleotides that occur widely in the

y
genomes of eukaryotes. When a retrotransposon is transcribed to produce

n
RNA and this RNA is translated, several enzymes are produced. These enzymes

t
make more DNA copies of the transposon by reverse transcription of the RNA,

O
then insert these copies into the cell’s chromosomes in random positions.

i
s
There are striking similarities between this method of propagating DNA in a

eukaryotic cell and the method used by retroviruses such as HIV to integrate

y
their genetic material into a host cell’s chromosomes. For retroviruses to
e
have evolved from retrotransposons, c apsid proteins would also have had to

p
evolve from host cell proteins.
v

2. Regressive hypotheses

Viruses develop from cells in a series of steps by loss of cell components.

o
i

This ts with the observation that both viruses and bacteria show variation in
n

complexity and self-reliance.

Some viruses are small and simple with few components, for example,
U

the polio virus. Others are much larger and more complex, such as the
n

smallpox virus. Mimivirus is an even larger example, with a diameter of

0.75micrometres and a genome of 1.2million base pairs. These large and

o
d

complex viruses have some enzymes of their own and perform functions that

most viruses leave to their host.

i
r

The cells of bacteria are expected to be self-reliant but there are parasitic
t
o

bacteria which replic ate inside a host cell. Some types of bacteria have
a

lost the ability to perform certain metabolic functions. For example, the

bacterium Chlamydia has a diameter of only 0.6micrometres and as few as

f

600 genes. At one time, Chlamydia bacteria were thought to be viruses but
x

they are cells with a cell wall and membrane. They are likely to have evolved
l

from an independent organism that bec ame parasitic, entering host cells and
O

reproducing inside them.

These observations suggest that viruses might have originated from

v

intraparasitic bacteria by loss of more and more life functions, including

respiration and protein synthesis.

E

Viruses may have arisen by various progressive and regressive routes. This would

help to explain their diversity. Shared features of viruses could be the result of

convergent evolution—they are shared for functional reasons rather than bec ause

of ancestry.

87
 Unity and diversity
LHA

N H O
N

s
N

N H N

s
e
N
N

r
N

diaminopurine thymine

y
H

▴ Figure 9 Scientists have discovered a bacteriophage (S 2-L) that uses the universal

l
y
genetic code with one dierence: it has diaminopurine instead of adenine in its DNA. The

n
letter Z is used for this modied base, so the DNA of the bacteriophage has Z–T base pairs

t
where other organisms would have A–T. This modic ation makes the DNA more heat-stable

O
and protects it from attack by the host. How does this aect our understanding of the origin

i
of viruses and the genetic code?

s
r

y
A2.3.6 R apid evolution in viruses
e
Viruses c an show extremely rapid rates of evolution. Even during an infection

p
of one person, a virus c an undergo heritable changes—it c an evolve. There are
v

three main reasons for this rapidity.

o
i

1. Evolutionary change c an only happen between one generation and the next,

so it is limited by generation time. In humans, the average generation time is

n

about 25 years but in viruses it c an be less than an hour.

2. Evolution depends on genetic variation. The ultimate source of this variation

U

is mutation and mutation rates tend to be high in viruses. This is particularly

n

true in RNA viruses such as coronaviruses, which do not perform any checks

or correct errors made during replic ation of their genetic material.

o
d

3. Evolution is the result of natural selection acting on variation in a

population. The intensity of natural selection on viruses tends to be high.

i

The host organism, whether a bacterium, plant or animal, has mechanisms

r

for detecting and destroying inv ading viruses. For example, antibodies in
o

humans target antigens such as proteins on the surface of the virus. If the
a

antigen changes, the antibodies no longer recognize it. Viruses with a new
f

variant of protein in the c apsid or in the enveloping membrane c an evade

u
x

the immune system and multiply, where as those with the previous form

are destroyed. As a consequence, natural selection is powerful and this

l

encourages rapid evolution.

O

▴
a

Figure 10 H1N1 inuenza viruses with

Two examples of rapid evolution are the inuenza virus and HIV.
haemagglutinin (H1) and neuraminidase
v

(N1) proteins visible in the enveloping

The inuenza virus

membrane
E

Inuenza is c aused by an enveloped virus that uses negative-sense single-

stranded RNA as its genetic material. It replic ates its genetic material using RNA

replic ase which, unlike DNA polymerase, does not proofread or correct errors.

This leads to a high mutation rate. Instead of a single RNA molecule, the genome

consists of eight separate molecules. Bec ause of this, a new strain of the virus

c an appear if a host cell is invaded by two dierent strains of the virus and some

RNA molecules from each strain are combined. The inuenza virus c an also be

88
 Cells

LHA
transmitted between species, particularly between birds and humans. This is

another c ause of new strains appearing frequently.

Tw o pro te i n s in the e nve l o pi n g me mb ra n e of the influenza vi r u s act as

antigens: h a e ma gg l u ti n i n is used to bi n d to a host cell, and n e u ra mi n i da s e

s
h e l ps with re l e a s e f ro m the host cell. These p ro te i n s c an c h a n ge and be pu t

to g e t h e r in n ew c o mb i n a t i o n s , c re a ti n g n ove l s t ra i n s of th e virus that h ave

s
th e p o t e n ti a l to c ause a pa n d e m i c . St ra i n s a re re fe r re d to by th e types of

e
c o m bi n a ti o n of th e s e pro te i n s . Fo r exa mp l e, Sp a n i s h flu in 19 18 was c aused

by H 1N 1 and Ho n g Ko n g flu in 19 6 8 was c aused by H3 N2 . R a pi d e vo l u ti o n

r
of th e i n fl u e n z a vi r u s exp l a i n s h ow a p e rs o n c an c o n tra c t influenza re pe a te dl y

and also w hy pro te c t i o n de pe n d s on v a c c i n a ti o n e ve r y ye a r. E ach v accine

y
c o n ta i n s s e ve ra l s t ra i n s of i n fl u e n z a vi r u s .

The HIV virus

l
y

n
HI V is a re trovi r u s th a t uses re ve rs e tra n s c r i p ta s e to c o nve r t its s i n g l e - s t ra n de d

RNA genome to D NA . Th i s e n z y me does not pro o f re a d or c o r re c t e r ro rs

t
(u n l i ke D NA p o l y m e ra s e), l e a di n g to ma ny m u t a ti o n s . Mutations a re also

O
i
c aused by cytidine de a m i n a s e, an enzyme ma de by th e host that c o nve r ts

s
cytosine to u ra c i l . Th e s e tw o f a c to rs to ge th e r g i ve HIV the highest k n ow n

mu t a t i o n ra t e of a ny vi r u s . Eve n within a pe rs o n i n fe c t e d by one s tra i n of H I V,

y
mu t a t i o n s will pro d u c e m a ny ge n e ti c a l l y di ffe re n t s t ra i n s . Wh e n e a host cell is

i nv a d e d by two of mo re di ffe re n t s t ra i n s , the v i ra l ge n e s c an c o mb i n e l e a di n g

p
to e ve n m o re d i ve rs i t y.
v

Most of the mutations that occur in HIV are harmful to the virus, so the action of

cytidine deaminase may be protective to the host. Even so, the rapid generation of
o
i

new strains within a person helps the virus to evade the immune system. As a result,
n

most infections are chronic rather than curable. HIV has a protein on its surface that

it uses to bind to and enter a host cell. Mutations in the env gene that codes for this
U

protein allow HIV to evolve to use dierent cell types in the human body as hosts.
n

HIV can also evolve to become resistant to the antiretroviral drugs used to treat

patients infected with HIV, so a combination of two or more drugs is necessary.

o
d

years aer becoming HIV+

i

0.2
r

5.9

0.7
t

7.9
o

1.2
8.9
a

2.2
9.9
f

5.3
u
x

l
O

◂ Figure 11 This tree diagram shows how

v

the env gene evolved in one patient over

the 10-year period aer they bec ame HIV-

E

positive. E ach dot represents a new version

Source: Dapp MJ, Kober KM,

of the gene, with the colour showing when

Chen L, Westfall DH, Wong K,

it was rst identied. A change in colour in

et al. (2017) Patterns and rates of

the branches on the tree diagram shows that

viral evolution in HIV-1 subtype

the env protein would bind to a dierent

B infected females and males.

PLOS ONE 12(10): e0182443 host cell protein

89
 Unity and diversity
LHA

Data-based questions: Progression in HIV infection

HIV targets CD4 T-cells in humans. These cells are part 1. Describe the changes in CD4 T-cell numbers in a

of the immune system used to ght infectious disease. patient with typic al progression of the infection. [3]

−3

s
When the level of CD4 cells falls below 200 cells mm of
2. Compare and contrast the levels of virus found

blood, the infected individual begins to display a number

in the blood in typic al progressors and long-term

s
of relatively rare opportunistic infections. At this point,
survivors. [3]

an HIV-infected individual is said to have AIDS (acquired

e
3. Determine the length of time it takes for AIDS to

immunodeciency syndrome). Individuals vary in their

develop in:

r
response to HIV infection. The four graphs in Figure 12

a. typic al progressors [1]

show the CD4 concentration (thick curves with black

P
b. rapid progressors. [1]

y
squares) and level of HIV in the blood (thin curves) for

4. Suggest two reasons for the dierences in the

patients typic al of four dierent types of progression.

l
progress of the disease in dierent individuals. [2]

n
typic al progressors long-ter sriors

1,200 1,200

O
1,000 1,000

i
3

sllec-

sleel
800 800

s
500 500

o
r


400 400
4D

e
200 200

p
v

0 3 6 9 12 1 2 3 4 5 6 7 8 9 10 11 0 3 6 9 12 1 2 3 4 5 6 7 8 9 10 11

weeks years weeks

o years
i
n

long-ter non-progressors
rapid progressors

1,200 1,200

1,000 1,000
U
3

sllec-

sleel
800 800
n

600 600

o
o


d

400 400
Death
4D

200 200
i
r

0 3 6 9 12 1 2 3 4 5 6 7 8 9 10 11 0 3 6 9 12 1 2 3 4 5 6 7 8 9 10 11
o

weeks years weeks years

a

▴
f

Figure 12
u
x

Data-based questions: COVID-19

O

Figure 13 shows results of an investigation into the origin of COVID-19 is organized. Genes S, E, M and N code for
v

of COVID-19. This investigation was c arried out during the four structural proteins: spike, membrane, envelope

the early stages of the pandemic c aused by this virus. and nucleoc apsid. Other regions, c alled open reading
E

The graph shows how similar COVID-19 is to ve other frames (ORF), have numbers ranging from 1a to 8 and

coronaviruses. The chart above shows how the genome contain varying numbers of genes.

90
 Cells

LHA
1. State how many bases there are in the genomes of 4. Compare and contrast the genome of Bat SARSr-CoV

these coronaviruses. [1] HKU3-1 with the genomes of the other coronaviruses,

including COVID-19. [3]

2. Predict, with a reason, which part of the coronavirus

genome contains the most genes. [2] 5. a. Deduce which part of the COVID-19 genome is

s
least similar to that of the other viruses. [1]
3. Deduce, with a reason, which of the other

coronaviruses COVID-19 is most closely related to. [2] b. Suggest a reason for this part of the genomes

s
varying the most. [1]

e
r
ORF1a
ORF1b

y
E 6 8

5,000 10,000 15,000 20,000 25,000 30,000

l
y
genome nucleotide position

n
t
100

O
i
90

s
% /

80

r
y t i t n ed i

y
e
70

p
ed i t o e l c u n

60

o
SARSo 01
i

50 t o R 13

n

t o 45

40
t SARSo1

t SARSo 31

U

0 5,000 10,000 15,000 20,000 25,000 30,000

genome nucleotide position

o
d

▴ Figure 13 Source: Zhou, P., Yang, XL., Wang, XG. et al. A pneumonia outbreak associated with a new coronavirus of

probable bat origin. Nature 579, 270–273 (2020)

i
r

t
o

Linking questions
f

1. What mechanisms contribute to convergent evolution?

x

a. Using an example, explain the rapid evolution of viruses. (A2.3.5)

l
O

b. Outline the concept of analogous structures. (A3.2.8)

a

c. Explain what is meant by a selection pressure. (D4.1)

v

2. To what extent is the history of life characterized by increasing complexity

or simplicity?
E

a. Compare and contrast the structure of typic al prokaryotic and

eukaryotic cells. (A2.2.5 and A2.2.6)

b. Outline the theory of endosymbiosis. (A2.2.12)

c. Discuss the evidence for multiple origins of viruses. (A2.3.5)

91
 Unity and diversity

TOK

Are some things unknowable?

s
In some c ases, scientists have to struggle with hypotheses that self-replic ating molecules, compartmentalization, c atalysis

s
are dicult to test. Abiogenesis is the process by which life and polymerization. Researchers have been able to achieve

e
arose from non-life. It is impossible for researchers to replic ate all of these steps separately under laboratory conditions.

the exact conditions on prebiotic E arth, bec ause they are not

r
For example, researchers created solutions of nitrogenous

fully known and the rst protocells did not fossilize. In the early

bases, then dried the mixture on silicon wafers. They placed

1950s, Stanley Miller demonstrated that it was possible to

y
these samples in a simulation chamber (shown in Figure 1)

form amino acids from simple inorganic precursors. However,

and exposed them to wet-dry, day-night and seasonal

in the 70 or so years since then, scientists have been unable to

l
cycles, as well as to moisture, high temperature, oxidizing

create a simple life form from non-living precursors—despite

n
environments, high levels of radiation and other conditions

signic ant eorts.

that are thought to have been present on the prebiotic E arth.

t
To know something a priori is to know it through reason rather The purpose of these experiments is to investigate

O
i
than by observing it. Through reason, scientists agree that the emergence of self-c atalytic RNA molecules.

s
abiogenesis occurred and that it involved the emergence of

To know something a posteriori is to know it bec ause it has

y
e

p
v

o
i
n

C
U

n
o
d

i
r

◂ Figure 1 The planetary simulator at

o

McM aster University in Hamilton

a
f

u
x

l
O

a
v
E

◂ Figure 2 Sugars have been detected on

two dierent meteorites: NWA 801 and the

Murchison meteorite

92
 Cells

been observed directly. It is not possible to know the life in chemic ally and physic ally diverse environments.

biochemic al features of life on other planets a posteriori. The interface between the compartment and the

A priori, we know that life on other planets is likely to be surrounding environment would need to be semi-

based on c arbon, associated with water and cellular. This permeable to allow for exchange of waste and raw

reasoning is based on the following key factors: materials as well as communic ation.

s
• Molecular diversity is essential for life’s functions and

The strength of a theory comes from the observations it

s
for the process of evolution, and no other element c an

c an explain and the predictions it c an support. The theory

form as many different compounds or types of structure

e
of endosymbiosis—used to account for the evolution of

as c arbon.

eukaryotic cells—accounts for a wide range of observations.

r
• The subunits of the four major c ategories of biologic al
The theory that mitochondria originated as intracellular

molecule—including amino acids, nucleobases, the

mutualistic prokaryotes is supported by the observation of

y
components of lipids, and sugars — have all been found
intracellular parasitic bacteria such as Rickettsia, the c ause

in c arbon-rich meteorites.
of Rocky Mountain spotted fever. Within mitochondria,

l
prokaryotic type ribosomes, a prokaryotic type single
• No solvent dissolves a greater range of molecules

n
circular chromosome and double membranes all provide
than water. In addition, water is found throughout

empiric al evidence for the theory of endosymbiosis. Since

t
the universe. When planets form around stars, there

O
the original event occurred millions of years ago, the
is a tendency for them to contain large volumes of

i
phenomenon is not directly observable. However, bec ause
condensed water, and water exists as a liquid over a

s
the theory predicts and explains the observations, we hold it
relatively large temperature range.

to be a pragmatic truth—one that “works”.

y
• The compartmentalization that cells achieve is essential

to allow a living organism to maintain the conditions for

e

p
v

o
i
n

C
U

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

▴ Figure 3 The red cells in this micrograph are intracellular parasites in the cytoplasm of yolk sac cells

93
 Unity and diversity

End of chapter questions

1. Figure 1 represents a cell from a multicellular organism.

s
a. Identify, with a reason, whether the cell is:

s
i. prokaryotic or eukaryotic [1]

e
ii. part of a root tip or a finger tip. [1]

r
b. The magnific ation of the drawing is 2,500×

P
i. C alculate the actual size of the cell. [2]

y
ii. C alculate how long a 5 µm sc ale bar should

l
be if it is added to the drawing. [1]

y
▴ Figure 1

n
t

O
2. The electron micrograph in Figure 2 shows a section c. Organelle B is a contractile vacuole. Conduct

i
through a single Chlamydomonas reinhardtii green research and state the function of a contractile

s
alga. C. reinhardtii is a unicellular (single-celled) vacuole. [1]

r
organism used as a model system in genetics and

y
d. Structure E is c alled a pyrenoid. Figure 3 shows the

cellular motion studies.

e
growth rates of C.reinhardtii normal cells (purple)

p
a. Eight organelles are shown. Deduce the identity of and mutant cells that lack a pyrenoid (green), in air
v

the organelles labelled C, D, G and H. [4] with 5% CO and normal air with 0.04% CO
2 2

b. Organelle A is an eyespot. This is an organelle that i. Compare

o and contrast the growth rates of the

i

aids in the detection of light. When exposed to normal cells and the mutant cells at low CO
2
n

light, Chlamydomonas reinhardtii moves towards concentrations. [2]

the light. Suggest the adaptive advantage of this

ii. State the reason photosynthetic organisms

U

behaviour. [2]

require CO . [1]
2
n
o
d

A
i
r

B
t
o

C
f

u
x

D
l
O

E
v

F
E

▴ Figure 2

94
 Cells

f. Discuss what is signified by the error bars in

300
Key

Figure 3. [3]

normal cells
1–

yad

g. State the dependent and independent variables

mutant cells

100
ni

3–

in this example. [3]

mc
egnahc %

s
3. The microscope image in Figure 4 shows a rotifer
llyhporolhc

(centre bottom) and a filament of Spirogyra (right). The

100

s
longer numbered ticks on the sc ale are 122 µm apart.

e
a. The rotifer is multicellular, being composed of

0
about 1,000 cells. Discuss the advantages and

r
disadvantages of being multicellular. [4]

5% CO

P
air
2

y
b. Outline two quantitative and two qualitative

observations that c an be made from the

▴ Figure 3 Source: C aspari, O. et al. Pyrenoid loss in Chlamydomonas

l
micrograph. [4]
reinhardtii c auses limitations in CO2 supply, but not thylakoid

n
operating eciency, Journal of Experimental Botany, Volume

c. Estimate the length of the main body of the

68, Issue 14, 8 September 2017, Pages 3903–3913

t
rotifer [1]

O
i
d. Distinguish between the size of the rotifer cells and
iii. Suggest a possible function for pyrenoids

s
the size of the Spirogyra cells. [2]
based on the data. [2]

e. Deduce a possible combination of ocular and

r
e. Structure F in Figure 2 is a starch granule. Research

y
objective lens that were used to obtain this
and explain the reasons for storage of c arbohydrate
e
field of view. [1]
in photosynthetic cells as starch rather than

p
as sugar. [2]
v

o
i
n

C
U

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v

▴ Figure 4
E

95
 Unity and

s
d i v e rs i t y

s
e
r
3 Organisms

y
l
All living organisms h av e certain c h a ra c t e r i s t i c s in

n
common. Ta k e n t o g e t h e r, these c h a ra c t e r i s t i c s a l l ow

t
us to distinguish living organisms f rom non-living

O
i
things. All organisms re quire nutrition. Fo r ex a m p l e , the

s
plants in the background image use p h o t o sy n t h e s i s to

y
g e n e ra t e energy-rich compounds that form the basis
e
of the p l a n t ’s metabolism. D uring the past four billion

p
y e a rs , the E a r t h ’s e nv i r o n m e n t has changed d ra s t i c a l l y.
v

The d i v e rs i t y of life has been shaped by organisms’

o
i

evolutionary responses to these changes. The d i v e rs i t y

n

of life forms c an be accounted for by the p ro c e ss of

adaptive ra d i a t i o n .
U

Po p u l a t i o n s evolve and become adapted to their

e nv i r o n m e n t . The ability of a population to evolve

o
d

over m a ny g e n e ra t i o n s and adapt to its e nv i r o n m e n t

enables it to survive limiting f a c t o rs and the selection

i
r

p r e ss u r e s that arise when the e nv i r o n m e n t changes.

t
o

Ad a p t a t i o n s are inherited c h a ra c t e r i s t i c s that enhance an

a

o r g a n i s m ’s ability to survive in a particular e nv i r o n m e n t .

f

Every s u c c e ss f u l species is a c o m p l ex collection of

x

coordinate d adaptations produce d through evolutionary

l
O

p r o c e ss e s . Plants f rom the Sempervivum genus s h ow n in

a

the background image are typic al succulents in that they

v

are very d r o u g h t - t o l e ra n t and live for a long t i m e.

E
A3.1 Diversity of organisms

What is a species?

s
s
Biologists dene a species as a group of organisms with

shared traits that interbreed in the wild. How does this

e
denition work for organisms that reproduce asexually?

What other challenges exist with this denition? In 1859,

r
Charles D arwin wrote, “No one denition has satised

y
all naturalists; yet every naturalist knows vaguely what he

means when he speaks of a species”. What are the reasons

l
that establishing a denition of a species is so dicult? What

n
classic ation systems did early naturalists use? Consider the
▴ Figure 1 The light morph (le) and the “melanistic” or

two jaguars in Figure 1. To what extent is it surprising that

dark morph (right) of the jaguar (Panthera onca) interbreed in

t
they are considered to be the same species?
thewild

O
i
s
What patterns are seen in the diversity of genomes within and between species?

y
e
The genome is the whole of the genetic information

p
of an organism; that is, the total amount of DNA. In
v

what ways do genomes vary across the kingdoms of

o
life in terms of structure, composition, association with
i

proteins, loc ation, size, number of chromosomes? In

n

what ways does the genome within a species vary? The

Red visc acha rat is one of the few identied polyploid

animals. It has the highest chromosome number of

U

▴ Figure 2 The red visc acha (Tympanoctomys barrerae, le) and

any mammal, 102. Its closest living relative is Octomys

n

Octomys mimax, the Andean visc acha-rat of the same family (right)

mimax, the Andean visc acha rat (right), which has

56 chromosomes. Why is this condition more likely to

o
d

be found in plants?
i
r

SL and HL AHL only

t
o

A3.1.1 Variation between organisms as a dening feature of life A3.1.12 Diculties in applying the biologic al
a

A3.1.2 Species as groups of organisms with shared traits species concept to asexually reproducing species
f

A3.1.3 Binomial system for naming organisms and to bacteria that have horizontal gene transfer
u
x

A3.1.4 Biologic al species concept A3.1.13 Chromosome number as a shared trait

A3.1.5 Diculties distinguishing between populations and species within a species

l
O

due to divergence of non-interbreeding populations during speciation A3.1.14 Engagement with loc al plant or animal
a

A3.1.6 Diversity in chromosome numbers of plant and animal species species to develop a dichotomous key

A3.1.7 K aryotyping and karyograms A3.1.15 Identic ation of species from environmental
v

A3.1.8 Unity and diversity of genomes within species DNA in a habitat using barcodes

A3.1.9 Diversity of eukaryote genomes

E

A3.1.10 Comparison of genome sizes

A3.1.11 Current and potential future uses of whole genome sequencing

97
 Unity and diversity

A3.1.1 Variation between organisms as a

dening feature of life

An organism is an individual plant, animal, bacterium, or any other living thing.

The variety of organisms alive today is immense. Consider the dierences

s
between humans, trees growing taller than 100 metres, fungi that consist of

s
a network of narrow threads growing through the soil and brightly coloured

bacteria inhabiting volc anic pools at temperatures above 80°C and pHs

e
below 2. Even chimpanzees—animals to which we are closely related—are

dierent from us in many ways.

r
P
There is less variation among the members of a single species, but there are still

y
dierences between all individuals. There is least variation when two individuals

are genetic ally identic al. In humans, monozygotic twins are formed when a

l
zygote or early-stage embryo divides and develops into two individuals. Such

n
twins start out with the same genes but even they acquire dierences through

t
mutations and bec ause the environment in which they develop is never identic al.

O
i
The diversity of organisms adds to the richness of the natural world and helps to

s
make biology such a fascinating subject. Variation is also essential for the future of

▴ Figure 3 Even monozygotic twins show

life bec ause evolution by natural selection could not happen without it.

y
some dierences at birth and accumulate

more as they grow older

e

p
A3.1.2 Species as groups of organisms with
v

shared traits

o
i

If organisms in an area are studied, it soon becomes obvious that each individual
n

is a member of a group with recognizable traits or characteristics. These groups of

organisms are oen given a name in the local language, especially if they are used by

people or have an impact in other ways. For example, when Māoris arrived in New
U

Zealand about 800 years ago, they found tree ferns growing in the forests and used
n

them to build the walls of their houses. They recognized seven dierent types of tree

fern, which they named whekī, kuripaka, tuokura, mamuka, punui, ponga and kātote.
o
d

From the 17th century onwards, biologists used the term “species” for a group of

organisms with shared traits. Biologists have been naming and classifying species
i
r

ever since. C arl Linnaeus, who worked in the 18th century, was a pioneer of this
t
o

research. Linnaeus and other biologists of his time described the outer form and
a

inner structure of typic al members of a species. This is known as morphology. The

f

idea of a species as a group of organisms that share a particular outer form and
u

inner structure is the morphologic al concept of a species.

x

▴ Figure 4 The M āori name for these

If asked about the origins of species, Linnaeus and his contemporaries would
l

New Zealand tree ferns is ponga. The

O

scientic name is Alsophila dealbata. In probably have said that they were the work of a creator. They would have thought
a

addition to the seven species of tree fern

that each species was created from nothing and remained unchanged aer its

recognized by M āoris in New Zealand,

creation. When describing the morphology of species, early biologists believed
v

biologists have described three more:

they were looking at evidence of a creator ’s work.

Alsophila colensoi, Alsophila milnei and

E

Alsophila kermadecensis

A3.1.3 Binomial system for naming organisms

The international system that biologists use for naming species is c alled the

binomial system. E ach species name consists of two words, for example, Linnaea

borealis. The rst name is the genus name. A genus is a group of species that

have similar traits. The second name is the species or specic name.

98
 Organisms

There are various rules about binomial nomenclature:

• The genus name begins with an upperc ase (c apital) letter.

• The species name begins with a lowerc ase (small) letter.

• In typed or printed text, a binomial is shown in italics.

s
• After a binomial or genus name has been used once in a piece of text, it c an

s
be abbreviated to the initial letter of the genus name with the full species

name, for example, L. borealis

e
r
A3.1.4 Biologic al species concept

y
According to the morphologic al species concept, a species is an unchanging

group of organisms with clear dierences in external form and internal structure

l
y
between it and other species. However, this does not t with the concept of

n
evolution by natural selection proposed by Charles D arwin in 1857. Biologists ▴ Figure 5 Binomials are oen chosen to

t
honour a biologist, or to describe a feature
have looked for a new concept to describe species, but it has proved extremely

O
of the organism. Linnaea borealis is a small
dicult to nd a denition that ts all contexts. So far, at least 30 dierent

i
woodland plant that was named in honour
denitions have been suggested!

s
of C arl Linnaeus, the Swedish biologist who

The biologic al species concept denes a species as a group of organisms that introduced the binomial system and named

y
many plants and animals using it
c an successfully interbreed and produce fertile ospring. This concept explains
e
how a group of individuals c an exist as a coherent unit—the members of a species

p
interbreed and therefore share genes in a gene pool.
v

o
The biologic al species concept works well with some groups of organisms.
i

For example, the genus Allium contains hundreds of species, including onion
n

and garlic, but few interspecic hybrids have been reported in natural habitats

and these hybrids are usually sterile. The garden variety “Globemaster ” was

deliberately bred by crossing Allium christophii with Allium macleanii and is

U

sterile. Similarly, there are more than 600 species of conifer and interbreeding
n

between these species is very unusual. Where interspecic conifer hybrids

do occur, they are usually sterile. This is partly bec ause many conifers have no
o
d

close relatives, for example, Ginkgo biloba. In conifer genera where speciation

is occurring rapidly, such as junipers and pines, there is some interspecic

i
r

hybridization and it is less easy to identify species.

t
o

a
f

u
x

l
O

a
v
E

▴ Figure 6 Allium christophii (le), Allium Globemaster (centre) and Allium macleanii (right).

Globemaster is a hybrid of A. christophii and A. macleanii

99
 Unity and diversity

In other groups of plants and animals, the biologic al species concept is very

dicult to apply, due to geographic al separation and gradual divergence. This

is described in Section A3.1.5. Further diculties arise when migration brings

closely related but apparently distinct species together.

s
According to the biologic al species concept, hybridization of two species

suggests that those species are not distinct. For example, c aptive lions and tigers

s
have sometimes hybridized, producing ospring known as ligers (male lion

e
× female tiger) or tigons (male tiger × female lion). M ale ligers and tigons are

infertile but female hybrids are sometimes fertile. A rigorous interpretation of the

r
biologic al species denition would therefore consider lions and tigers to be the

same species, but this is not acceptable to biologists or the wider public.

y
l
y

n
t

O
i
s
▸ Figure 7 Polar bears (Ursus maritimus)

r
and grizzly bears (Ursus arctos horribilis) are

y
usually geographic ally separated but grizzly
e
bears are spreading north. If polar bears

p
and grizzly bears meet, they c an mate and
v

produce fertile ospring. The photo shows

o
such a hybrid
i
n

A3.1.5 Diculties distinguishing between

U

populations and species due to divergence

n

of non-interbreeding populations during

o
d

speciation
i

A population is a group of organisms of the same species, living in the same area,
r

at the same time. If two populations live in dierent areas, they are unlikely to
t
o

interbreed with each other. This does not necessarily mean that they are dierent
a

species. If they are physic ally and genetic ally similar, both populations are part of
f

the same species.

u
x

However, if two populations of a species do not interbreed, they c an diverge.

l

Recognizable physic al dierences may develop as the populations become

O

genetic ally more dierent. If dierences continue to accumulate, the two

a

populations may eventually become separate species. Bec ause this process is
v

usually very gradual, it c an be dicult to decide whether two populations have

become separate species and biologists sometimes disagree. (It would be

E

inappropriate to c arry out experiments with animal species to try to resolve these

issues.) The natural process by which species diverge to form new species is

c alled speciation. This is described in Topic A4.1.

100
 Organisms

s
s
e
r
P

y
l
y

n
▴ Figure 8 The sandwich tern Thalasseus sandvicensis (le) was rst recognized as a species by John Latham in 1787. C abot’s

tern (right) was classied as a subspecies of the sandwich tern but recent phylogenetic research suggests that it is a separate

t
species, Thalasseus acuavidus. Not all biologists agree. Populations of T. sandvicensis live in Europe whereas T. acuavidus

O
i
lives in North and South Americ a

s
r
A3.1.6 Diversity in chromosome numbers of

y
e
plant and animal species

p
A fundamental characteristic of any species is its chromosome number.
v

During the evolution of a species, this number c an change: it c an decrease if

chromosomes become fused together, or increase if splits occur. There are also
o
i

mechanisms that c an c ause the chromosome number to double. However,

n

changes to the chromosome number are rare and usually there is no change in a

species over millions of years.

U

In most plants and animals, body cells have an even number of chromosomes.
n

This is a consequence of sexual reproduction. A new life starts by fusion of a

male gamete and a female gamete, with each gamete containing one set of
o
d

chromosomes (9 in c abbages). This fusion of gametes produces a zygote with

two sets of chromosomes (18 in c abbages). All cells produced from the zygote
i
r

by mitosis inherit these two sets of chromosomes. Gametes with one set of
t

chromosomes are haploid. Body cells with two sets are diploid.
o

There is immense diversity in chromosome number among plants and animals.

f

It is useful to remember that humans have 46 chromosomes and chimpanzees,

u
x

our nearest relatives, have 48. You c an easily nd other chromosome numbers by

searching databases. They range from two to hundreds. Table 1 shows numbers
l
O

for some species.

a

Th e O xfo rd E n gl i s h D ictionary c o n s i s ts of 20 l a rge vo l u me s , e ach containing

v

i n fo r ma ti o n a bo u t the o r i gi n s and me a n i n g s of w o rd s . This i n fo r m a ti o n could

h ave been pu bl i s h e d in a s ma l l e r n u mb e r of l a rg e r vo l u me s or in a l a rge r

E

n u m be r of s ma l l e r vo l u me s . T h e re is a p a ra l l e l with th e n u mb e rs and sizes of

c h ro m o s o m e s in pl a n ts and animals. Some h ave a few l a rg e c h ro mo s o me s

and o th e rs h ave m a ny s ma l l ones. Re s e a rc h e rs exp e r i m e n te d by fusing th e

16 c h ro mo s o me s of ye a s t cells to re d u c e th e c h ro m o s o m e n u mb e r to 4 or

▴ Figure 9 Who has more

e ve n 2. Their f i n d i n gs s u g ge s t e d that th e a c tu a l n u mb e r of c h ro mo s o m e s in a

chromosomes—a dog or its owner?

s pe c i e s is not ve r y s i gn i f i c a n t , as long as all me mb e rs of th e species h ave th e

s a me n u mb e r.

101
 Unity and diversity

Data-based questions: Dierences in chromosome number

Plants Number Animals

no plant species yet discovered 2 Myrmecia pilosula ( jack jumper ant)

s
Haplopappus gracilis (in the aster family) 4 Parascaris equorum (horse threadworm)

s
Luzula purpurea (woodrush) 6 Aedes aegypti (yellow fever mosquito)

e
Crepis capillaris (in the aster family) 8 Drosophila melanogaster (fruity)

Vicia faba (eld bean) 12 Musca domestica (house y)

r
Brassica oleracea (c abbage) 18 Chorthippus parallelus (grasshopper)

P
Citrullus vulgaris (watermelon) 22 Cricetulus griseus (Chinese hamster)

y
Lilium regale (royal lily) 24 Schistocerca gregaria (desert locust)

l
Bromus texensis (Texas brome grass) 28 Desmodus rotundus (vampire bat)

n
Camellia sinensis (Chinese tea) 30 Mustela vison (mink)

Magnolia virginiana (sweet bay) 38 Felis catus (domestic c at)

O
Arachis hypogaea (peanut) 40 Mus musculus (mouse)

i
Coea arabica (coee) 44 Mesocricetus auratus (golden hamster)

s
Stipa spartea (porcupine grass) 46 Homo sapiens (modern human)

y
Chrysosplenium alternifolium (saxifrage) 48 Pan troglodytes
e (chimpanzee)

Aster laevis (Michaelmas daisy) 54 Ovis aries (domestic sheep)

p
Glyceria canadensis (manna grass) 60 Capra hircus (goat)
v

Carya tomentosa (hickory) 64 Dasypus novemcinctus (armadillo)

o
i

Magnolia cordata (a small deciduous tree) 76 Ursus americanus (Americ an black bear)
n

Rhododendron keysii (evergreen shrub) 78 Canis familiaris (dog)

▴ Table 1
U

1. There are many dierent chromosome numbers in Table 1 but some numbers are not seen, for example,
n

5, 7, 11 and 13. Explain why none of the species has 13 chromosomes. [3]

2. Using the data in Table 1, discuss the hypothesis that there is a positive correlation between the number of
o
d

chromosomes in a species and its complexity. [4]

3. Explain what makes it impossible to c alculate the genome size of a species from its chromosome number. [1]
i
r

4. Using the data in Table 1, identify a change in chromosome structure that may have occurred during human evolution. [2]
t
o

a
f

u
x

A3.1.7 K aryotyping and karyograms

l

The chromosomes of an organism become visible when Chromosomes are classied based on three types of
O

cells are dividing, with metaphase giving the clearest dierence:

view. To study the chromosomes of an organism, cells

• Some stains give chromosomes distinctive banding

v

are stained and placed on a microscope slide. They are

patterns, with different banding in each type of

burst to spread the chromosomes by pressing on the

E

chromosome.

cover slip. The chromosomes oen overlap each other

• Chromosomes vary in size. In humans, the largest

but with c areful searching, it is usually possible to nd a

(chromosome 1) is more than five times longer than

cell with no overlaps. The stained chromosomes c an then

the shortest (chromosome 21).

be photographed. Originally, analysis involved cutting

out each chromosome from a print and arranging them

• E ach chromosome visible in metaphase consists

manually. This process c an now be done digitally.

of two strands c alled chromatids, held together

102
 Organisms

by a centromere. The position of

the centromere varies. In some

chromosomes it is near the centre,

so the arms of the chromosomes are

s
equal length. In other chromosomes

s
the centromere is nearer to one end,

so the chromosome has a shorter and

e
a longer arm.

r
The characteristic types of chromosome

in a species are c alled the karyotype.

y
An image showing the karyotype of an

organism is c alled a karyogram. The

l
chromosomes are arranged in pairs,

n
starting with the longest pair and ending

with the smallest.

O
i
s
▴ Figure 10 K aryogram of a human female, with uorescent staining to generate

y
banding patterns
e

p
v

o
i

Data-based questions: Primate chromosome numbers

n

Human somatic (body) cells have 46 chromosomes. Our closest primate

2
U

relatives—chimpanzees, gorillas and orangutans—all have 48. Human chromosome

12
n

types are numbered from 1 to 22. One hypothesis is that human chromosome 2 was

formed from the fusion of two chromosomes in a primate ancestor. Figure 11 shows

banding patterns of human chromosome2 compared with chromosomes 12 and 13

o
d

from chimpanzees.
i
r

1. Compare human chromosome 2 with the two chimpanzee chromosomes. [3]

t

2. The ends of chromosomes,

o

c alled telomeres, have many repeats of the

a

same short DNA sequence. If the fusion hypothesis were true, predict

what would be found in the region of the chromosome where the fusion
f

is hypothesized to have occurred. [2]

x

3. Normally a chromosome has just one centromere, but in chromosome 2

l
O

there are remnants of a second centromere. Explain this observation. [2]

a

4. Discuss the strength of the evidence for a fusion of chimp chromosomes

13
v

in the evolution of chromosome 2 in humans. [3]

▴ Figure 11 Human
E

chromosome 2 (le) aligned

with chimpanzee chromosomes

12 and 13 (right)

103
 Unity and diversity

F alsic ation: Testable versus non-testable statements

The nature of scientic theories enables both

explanations and predictions. When enough

s
observations are predicted and explained by

a theory, it becomes the consensus. If a new

s
observation or experimental result is not well

e
explained or predicted, the theory is either

enhanced to address the observation, or

r
considered falsied.

James Hutton (1726–1797) developed the

y
theory that geologic al features were not xed

but underwent constant transformation over

l
long periods of time. He argued that the

n
E arth’s history c an be inferred from evidence in

present-day rocks and that the E arth must be

O
much older than predictions based on biblic al

i
chronology. No biblic ally reconstructed date

s
▴ Figure 12 The lower layers of rock in this drawing contain evidence of
for the creation of the E arth was early enough to

marine life. The striated appearance indic ates many years of sediment being
t with the huge timesc ale implied by geology,

y
laid down, followed by a geologic al event that changed their orientation
zoology and paleontology.

from vertic al to horizontal. Aer being partly eroded away, these layers were
e
Knowledge claims based on religious faith

p
subsequently covered by further layers of sediment. Hutton used observations

are oen not falsiable by observation or

of rock formations such as this to support the theory that geologic al features
v

experimentation. This is not to say they are

were not xed but underwent transformation over long periods of time

not valid; rather, they are not testable. For

o
i

omnipotence meant he could c ause long geologic al ages

example, Hutton’s observations were explained
n

to occur in short periods of time.

by the notion that the biblic al “days” were metaphoric al

and corresponded to much longer periods of time (the You have learned about the theory that the human
U

“interval theory”). Another thinker proposed that God’s chromosome 2 arose from fusion of chromosomes 12 and

13 in an ancestral primate. Is this theory testable?

n
o
d

A3.1.8 Unity and diversity of genomes

i
r

within species
t
o

Among biologists today, the word “genome” means all of the genetic

information of one individual organism or group of organisms. Genetic

f

information is contained in DNA, so the genome is the entire base sequence of

x

each of the DNA molecules (chromosomes).

l
O

A genome contains functional units c alled genes. A gene is a length of DNA

a

c arrying a sequence of hundreds or even thousands of bases. Typic ally, the

members of a species have the same genes, in the same sequence, along each
v

of their chromosomes. This allows parts of the chromosomes to be exchanged

during meiosis, promoting genetic diversity in a species without any genes being
E

omitted or duplic ated. The genome of a species and the arrangement of genes

on the chromosomes is thus an illustration of the unity in living organisms.

Diversity in the genomes of a species is largely due to variation in individual

genes. Alternative forms of a gene, c alled alleles, oen exist within a species.

The alleles of a gene dier from each other in base sequence. Usually only one

104
 Organisms

or a very small number of bases are dierent—for example, one allele might have

adenine at a certain base position while another allele might have cytosine in that

position. Sometimes larger sections of a gene become altered, but this usually

results in loss of gene function.

s
Positions in a gene where more than one base may be present are c alled single-

nucleotide polymorphisms, abbreviated to SNPs and pronounced “snips”.

s
M any thousands of individual human genomes have been sequenced, allowing

e
researchers to assess the frequency of SNPs. More than 100 million dierent SNPs

have been discovered so far in human genomes. This seems a huge number but

r
remember there are over threebillion base pairs in our genome. Most bases are

therefore the same in all humans—another illustration of unity.

y
Within one individual, there are typic ally about 4,000–5,000 SNPs, so only about

l
1 base in 650,000 is dierent from that commonly occurring in humans. This may

y
seem a low level of diversity but these SNPs are the main factor in making humans

n
dierent from each other (unless we have an identic al twin!).

O
i
These positions are These bases vary in feer

s
regarded as single- than 1% of individuals f a

r
nucleotide polymorphisms different base is present it

y
(SNPs) bec ause at least 1% of is regarded as a mutation
e
individuals have a different rather than an SNP

p
base from the others
v

o
i
n

paternal allele TT

maternal allele TT

U

The child is homoygous for this The child is heteroygous for

o
d

SNP bec ause the alleles inherited this SNP bec ause the alleles

from their parents have the same inherited from the mother and
i

◂ Figure 13 SNPs are inherited from

r

base father have a different base

our parents
t
o

a
f

A3.1.9 Diversity of eukaryote genomes

u
x

The genomes of plants, animals and other eukaryotes vary by a huge amount,
l

both in the overall size of the genome and in base sequences. Variation between
O

species is far larger than genome variation within a species.

a

Variation in genome size

v

O verall genome size is measured in base pairs. There is a huge range in genome
E

size and some species have a surprising amount of DNA. L arge genomes c an

contain a lot of non-functional DNA, so they do not necessarily contain more

functioning genes than smaller genomes. For example, about half of the human

genome consists of transposons (transposable sequences), most of which have

no known function. Transposons are sometimes referred to as “junk DNA”.

105
 Unity and diversity

Table 2 shows the range of genome sizes in dierent organisms.

Organism Genome size / Description

million base pairs

s
Paramecium tetraurelia 27 Unicellular organism

s
Apis mellifera 217 Honey bee

e
Homo sapiens 3,080 Human

Pan troglodytes 3,175 Chimpanzee

r
Paris japonica 150,000 Woodland plant

y
▴ Table 2

l
y

n
Variation in base sequence

t
Two populations of a species will have some dierences in base sequence.

O
If these populations diverge to form separate species, more dierences will

i
accumulate over time. In some genes, changes in base sequence are infrequent.

s
These tend to be genes with a vital function that does not change—for example,

r
the gene for the protein cytochrome c, which has an essential role in respiration.

y
As a result, there may be relatively few (or no) base sequence dierences, even
e

p
between distantly related species.
v

Dierent species also have dierent numbers and types of genes. Genes c an be

o
added to a genome or removed from it, so species that diverged from a common
i

ancestor hundreds of millions of years ago have developed dierences in their

n

genetic make-up, especially when they are adapted to dierent ways of life.
U

n
o
d

i
r

t
o

a
f

u
x

▴ Figure 14 You c an use the GenBank website to compare base sequences of specic genes between species. This image

shows the rst 120 bases in the sequences of the gene that codes for cytochrome oxidase 1 in nine species. The sequences have
l

been aligned using additional soware to allow comparison

O

a
v
E

106
 Organisms

Data-based questions: Genome sizes

The graph in Figure 15 compares genome size with the 5.0

rebmun
number of genes that code for proteins in species of

s
eukaryote.

eneg
1. What trend does the data in the graph show? [2]

s
4.0

2. The curve that has been t to the graph shows that

gnidoc-nietorp

e
the number of protein-coding genes is not directly

proportional to genome size.

r
3.0
a. What trend line on the graph would indic ate

y
direct proportion between the variables? [1]

01
gol
b. Discuss the reasons for the number of protein-

l
coding genes not being directly proportional

y
2.0

n
to genome size. [2]
2.0 4.0 6.0

t
2
log genome size / kbp
10
3. The statistic R has been c alculated for this data

O
i
and is 0.919.

▴ Figure 15

s
2

a. What is the statistic R ? [1]

Source: Hou Y, Lin S (2009) Distinct Gene

r
Number-Genome Size Relationships for

b. What does a value as high as 0.919 indic ate? [2]

y
Eukaryotes and Non-Eukaryotes: Gene
e
Content Estimation for Dinoagellate
4. The sc ales on the axes are logarithmic.

p
Genomes. PLOS ONE 4(9): e6978.

a. If the log protein-coding gene number is 4.0,

v

10

what is the actual number of protein-coding

genes? [1]
o
i
n

b. If the log genome size (kbp) is 6.0, what is the

10

actual number of base pairs? [2]

U

n
o
d

A3.1.10 Comparison of genome sizes

Knowledge of the size of genomes c an form the basis a. Plant DNA C-values D atabase hosted by Kew
i
r

of research into genome evolution. It c an also be used Gardens (https://cvalues.science.kew.org.com)

t
o

to estimate the cost and diculty of future genome

b. Animal Genome Size Database (www.genomesize.com)

a

sequencing programmes. Genome sizes are typic ally

f

c. Fungal Genome Size D atabase (www.zbi.ee/fungal-

given as nuclear DNA contents of a haploid cell such
u

genomesize.com)
as a gamete (C-values), either in units of mass (usually
x

−12

picograms; 1 pg = 10 grams) or in number of base pairs

d. Microbial Genomes (https://www.ncbi.nlm.nih.gov/
l

or megabase pairs (1 Mbp = 10 base pairs).

O

genome/microbes.com)
a

Nuclear DNA content data for more than 10,000 species

of plant, animal, fungus and microbe is available from

v

these four independent databases:

E

107
 Unity and diversity

ATL Thinking skills: Evaluating alternative perspectives

Knowledge claims are aected by criteria for judgment. regulation of gene expression. Are organisms with

For example, the answer to the question, “How does many tissue types more complex than organisms with

s
genome size correlate with complexity?” depends on our fewer tissue types?

criteria for judgement. In particular, what do we mean

• Single-celled organisms c arry out many different

s
by “complexity”?
activities per cell, while a single cell within a

e
D aniel W. McShea, a paleobiologist at Duke University multicellular organism c arries out a smaller range of

quoted in Scientic American, discusses the problems activities. Does that make singled-celled organisms

r
with the term complexity: “It’s not just that they don’t more complex?

know how to put a number on it. They don’t know what

• More recently evolved organisms often have a

y
they mean by the word”.
greater number of novel adaptations than those

For example:
which evolved longer ago. Does this make them

l
• Plants are metabolic ally more complex than animals. more complex?

n
• Multicellular organisms have a greater diversity of

Until we agree on a denition of the term “complexity”,

t
cell types than prokaryotes, due to more complex

c annot agree on an answer to the question.

O
i
s
r

y
Thinking skills: Answering open-ended questions
e
ATL

p
A database is an organized collection of data stored suggests the method to be followed. The dependent and
v

electronic ally in a computer system. D ata mining is independent variables should be easy to identify from the

o
i

a process used by researchers to turn raw data into question. For example:

useful information. M any successful internal assessment

n

a. Do angiosperms, on average, have larger genomes

investigations and extended essays in biology have been

than pteridophytes?

based on inquiries c arried out using databases.

U

b. Do fungi and animals have similar genome sizes?

In both types of project, it is essential to begin with
n

an open-ended question. An open-ended question

Generate a research question about genome size and test

c annot be answered with a simple “yes” or “no” and the

it using one or more databases.

o
d

researcher does not know the answer before they start.

The clearest questions are expressed so that the wording

i
r

t
o

a
f

A3.1.11 Current and potential future uses of

u
x

whole genome sequencing

l

Whole genome sequencing is determining the entire base sequence of an

O

organism’s DNA. This was rst done in the 1990s with bacteria and archae a,

bec ause their relatively small genomes made it e asier. It is now fe asible with
v

most organisms. Some of the e arly landmarks in whole genome sequencing are

shown in Table 3.
E

108
 Organisms

Year Organism Number of base pairs

1995 Haemophilus inuenzae (a pathogenic bacterium)—rst prokaryote 1.8 million

1996 Saccharomyces cerevisiae (yeast—a unicellular fungus)—rst eukaryote 12 million

1998 Caenorhabditis elegans (a nematode worm)—rst multicellular organism 100 million

s
2000 Arabidopsis thaliana—rst plant 135 million

s
2003 Homo sapiens—complete sequence published 3,080 million

e
▴ Table 3

r
Look at the data in Table 3. In less than 10 years, the size of the genomes being

y
sequenced increased by a factor of a thousand. This was made possible by

technologic al developments which both increased the speed of sequencing and

l
reduced the cost. These developments have continued. The cost of sequencing

y
one human genome, for example, has dropped from $100 million in 2001 to less

n
than $1,000 in 2020.

O
There has also been exponential growth in the number of species for which at

i
least one sequence has been completed, so any gure quoted for the number

s
of complete genome sequences will soon be exceeded. The E arth BioGenome

r
Project aims to sequence the genomes of all known species.

y
e
A principal goal of sequencing the genomes of a wide range of species is

p
investigation of evolutionary origins. Comparisons between genomes allow
v

researchers to identify relationships between species and trace the diverging

o
pathways from common ancestors. Knowledge gained from studying the genomes
i

of dierent species will make it easier to conserve and protect biodiversity.

n

Research into the genomes of pathogenic bacteria and viruses will help in the

control and prevention of infectious diseases caused by these organisms.

U

There are ambitious aims for sequencing more genomes of individual humans.
n

So far, over one million individual human genomes have been sequenced, and

this number has been doubling about every eight months. This has increased
o

understanding of human origins and migrations in all parts of the world. It is also
d

providing more data than ever about genetic diseases and genes that aect
i

human health. In future, it may be possible to sequence the genome of every

r

person. This could lead to the development of personalized medicine. If it is

t
o

known which SNPs and other genetic features are present in a person’s genome,
a

it will be easier to predict health problems and prescribe appropriate drugs and
f

other treatments for that person.

u
x

l
O

a
v
E

◂ Figure 16 Sequencing read

from the DNA of the Pinot Noir

variety of grape

109
 Unity and diversity
LHA

A3.1.12 Diculties in applying the

biologic al species concept to asexually

reproducing species and to bacteria that

s
have horizontal gene transfer

s
The biologic al species concept works well with many groups of species.

However, it works less well with species that reproduce asexually or have

e
methods of horizontal gene transfer.

r
Asexually reproducing species

y
If members of a species interbreed by sexual reproduction, their traits are

remixed every generation. This prevents the development of signic ant

l
dierences between individuals. Shared traits allow members of the species to

n
be identied. M any species reproduce both sexually and asexually, but as long as

they sometimes reproduce sexually, they will remain as a coherent and therefore

t
unied group.

O
i
Some species—such as blackberries (Rubus fruticosus) and dandelions

s
(Taraxacum ocinale)—only reproduce asexually. Both these plant species

r
produce owers and look as though they are reproducing sexually but ospring

y
are actually produced by mitosis and are genetic ally identic al to the parents.
e

p
All ospring produced by asexual reproduction are clones of their parent.
v

If a clone does not interbreed with other clones, it is a separate species

o
according to the biologic al species concept. M any dierent clones may be
i

recognized. Among blackberries, for example, hundreds of clones have been

n

named as separate species. Only a few experts c an distinguish between these

“microspecies” and great eorts are made to conserve some of the rarer clones.
U

A better policy is to recognize that blackberries, dandelions and other species

that have abandoned sexual reproduction are no longer species according to the
n

biologic al species concept.

o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

▴ Figure 17 The yellow ower head of a dandelion ▴ Figure 18 The dandelions in this eld may all be

develops into a spheric al array of wind-dispersed members of the same clone. They are owering and

fruits, each with a single seed. Bec ause they have been producing seed asexually so they are not a typic al

produced asexually, all the seeds are genetic ally identic al biologic al species

110
 Organisms

LHA
Species with horizontal gene transfer

The evolution of life is oen thought to resemble a tree, starting with a single

trunk from which branches emerge. Repeated branching eventually leads to

individual species. Once formed, a branch remains separate and does not rejoin

s
other branches. In the same way, species do not interbreed with other species so

their genes remain separate.

s
However, genome sequencing has revealed that the separation between species

e
is not always complete. Genes are sometimes transferred from one species to

another, even between distantly related species. This process is c alled horizontal

r
gene transfer, to distinguish it from vertic al transfer from parent to ospring.

y
Horizontal gene transfer is frequent among bacteria. For example, it is how

antibiotic resistance genes c an move from one species to another. In fact,

l
there is so much gene transfer between bacteria that it is debateable whether

n
the biologic al species concept (or any other species concept) works with

t
prokaryotes. Among eukaryotes, although horizontal gene transfer has occurred,

O
it is less frequent and species are easier to dene.

i
s
r

y
e

p
v

o
i
n

C
U

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

◂ Figure 19 D arwin’s famous evolutionary

tree diagram, drawn in about 1837 in one of

his notebooks

111
 Unity and diversity
LHA

A3.1.13 Chromosome number as a shared

trait within a species

E arlier in this topic, you learned that the members of a species usually have

the same number of chromosomes. This lack of diversity is a consequence of

s
reproducing sexually rather than asexually.

s
For sexual reproduction to occur, males and females of the species produce

e
gametes. These gametes have the haploid number of chromosomes (for

example, 23 in human eggs and sperm). In eukaryotes, these gametes are

r
formed my meiosis, which halves the chromosome number. M ale and female

P
gametes then fuse to produce a zygote with the diploid number of chromosomes

y
(46 in humans).

l
In a diploid nucleus, there are two sets of chromosomes and each chromosome

n
c arries the same sequence of genes as one other chromosome. Two

chromosomes c arrying the same sequence of genes are said to be homologous.

O
During meiosis, homologous chromosomes pair up with each other, so they c an

i
be reliably separated into dierent daughter cells. The separation of homologous

s
chromosomes into separate daughter cells halves the chromosome number.

r
If two organisms with dierent chromosome numbers mated and produced

y
ospring, the ospring would almost certainly have problems in carrying out
e

p
meiosis. Some of the chromosomes would not be able to pair up because they

would not be homologous to any other chromosome. As a result, there would not
v

be an orderly segregation of chromosomes into two groups. The cells produced

o
i

by meiosis would not be viable and gametes could not be produced. This is why

ospring of parents with dierent chromosome numbers are usually infertile.

n

C
U

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

▴ Figure 21 All the cells in these Bramley

▴ Figure 20 These owers are on a Bramley

apples are triploid, like the tree on which they

apple tree, which is triploid, with 51 chromosomes

grew. Bramley apple trees can produce fruit even

instead of the usual 34. Meiosis therefore fails and

though they cannot carry out meiosis, because

the anthers in the owers produce no pollen, so a

cells in the fruit are produced by mitosis

Bramley c annot pollinate any other apple tree

112
 Organisms

LHA
Data-based questions: Chromosome numbers in Sphagnum mosses

Researchers c an estimate the DNA content of cells by 1. Compare the DNA content of the bog mosses. [2]

using a stain that binds specic ally to DNA. A narrow

2. Suggest a reason for six of the species of bog moss

s
beam of light is passed through a stained nucleus and the

on the Svalbard islands having the same number of

amount of light absorbed by the stain is measured. This

chromosomes. [2]

s
gives an estimate of the quantity of DNA. Table 4 shows

3. S. arcticum and S. olai probably arose as new

such estimates for leaf cells in eight species of bog moss

e
species when meiosis failed to occur in one of their
(Sphagnum) on the Svalbard islands.

ancestors.

r
Sphagnum M ass of Number of

a. Deduce the number of chromosomes in a leaf cell

P
species DNA / pg chromosomes

y
nucleus of these species. Give two reasons for

S. aongstroemii 0.47 19

your answer. [3]

l
S. arctium 0.95

y
b. Suggest a disadvantage to S. arcticum and

n
S. balticum 0.45 19

S. olai of having more DNA than other

t
S. mbriatum 0.48 19
bog mosses. [1]

O
i
S. olai 0.92
4. It is unusual for plants and animals to have an odd

s
S. teres 0.42 19 number of chromosomes in their nuclei. Explain how

mosses c an have odd numbers of chromosomes in

S. tundrae 0.44 19

y
their leaf cells. [2]

S. warnstori 0.48 19
e

p
▴ Table 4
v

o
i

A3.1.14 Engagement with loc al plant or animal species to develop a

n

dichotomous key
U

Dichotomous keys are constructed for identic ation of species within a group. A dichotomy is a division into two; a
n

dichotomous key consists of a numbered series of pairs of descriptions. In each pair, one description should clearly

match the species and the other should clearly be wrong. The features that the designer of the key chooses to describe
o
d

must therefore be reliable and easily visible. E ach pair

of descriptions leads either to another numbered pair

i
r

in the key, or to an identic ation. An example key is

t

shown in Figure 22.

o

Keys are usually designed for use in a particular area.

All the groups or species found in that area c an be

bear wolf fox c at dog
f

identied using the key. There may be a group of

x

organisms in your area for which a key has never been

designed. Choose from these suggestions or come up

l
O

with your own idea:

a

• trees in the loc al forest or on your school c ampus,

duck rabbit / hare squirrel deer heron

v

using descriptions of leaves or bark

• water plants in a loc al pond

▴ Figure 22 These images show the right front footprints of 10 types
E

of mammal and bird (not to sc ale). They c an be used to develop skills in

• birds that visit bird-feeding stations in your area

constructing dichotomous keys

• invertebrates that are associated with one

particular plant species.

113
 Unity and diversity
LHA

ATL Communic ation skills: Construction of dichotomous keys for use in identifying

specimens

The distinguishing features described in a dichotomous visible. They are not, so you are directed to step 6 of the

s
key must be reliable and easily visible. An example key is key. You must now decide if the species has a blowhole. It

s
shown in Figure 23. We can use it to identify the species does not, so it is a dugong or a manatee. A fuller key would

in Figure24. In step 1, you must decide if hind limbs are have another step to separate dugongs and manatees.

e
1 Fore and hind limbs visible, c an emerge on land........... 2

r
Only fore limbs visible, c annot live on land................... 6

y
2 Fore and hind limbs have paws................................... 3

Fore and hind limbs have ippers................................ 4

l
3 Fur is dark................................................................ sea otters

n
Fur is white............................................................... polar bears

t
4 External ear ap visible............................................ sea lions and fur seals

O
No external ear ap.................................................. 5

i
5 Two long tusks......................................................... walruses

s
No tusks................................................................... true seals

y
6 Mouth breathing, no blowhole.................................. dugongs and manatees
e
Breathing through blowholes.................................... 7

p
7 Two blowholes, no teeth.......................................... baleen whales
v

One blowhole, teeth................................................. dolphins, porpoises and whales

o
i

▴ Figure 23 A dichotomous key to groups of marine mammals

n

C
U

n
o
d

i
r

t
o

a
f

u
x

l
O

▴ Figure 24 A marine mammal, photographed in Florida

v
E

114
 Organisms

LHA
A3.1.15 Identic ation of species from

environmental DNA in a habitat using

barcodes

s
DNA barcodes are short sections of DNA from one gene, or at most several

genes, which are distinctive enough to identify a species. For example, part

s
of the gene for cytochrome oxidase subunit 1 is used as a barcode for animal

e
species. DNA barcoding allows scientists to identify species from small pieces
▴ Figure 25 E arly warnings of the spread

of tissue that might otherwise be dicult to recognize. For example, many plant
of diseases c an be obtained by regular

r
species have leaves that are oval with a pointed end. Barcodes make it possible sampling of wastewater and testing for DNA

to distinguish these species. of pathogens. This technique has been used

y
to test for new strains of COVID-19 and for

Species identic ation is now possible using environmental DNA, collected from
resurgence of polio

l
water, soil or any other part of the abiotic environment. Typic ally, this contains

n
DNA from a wide diversity of organisms that have interacted with the sampled

environment. DNA barcodes c an be used to identify these organisms. This

t
technologic al advance has many applic ations in ecology and conservation.

O
i
In a recent c ase, samples taken from waterholes in northern Australia were

s
analysed using DNA barcodes. This analysis showed that Gouldian nches

r
(Erythrura gouldiae), an increasingly rare bird species, had visited the waterholes.

y
In another c ase, DNA le in snow tracks was used to conrm the presence of a
e
small c arnivorous mammal c alled a sher (Pekania pennanti) in Idaho.

p
v

o
i
n

▴
U

Figure 26 Tracks of a sher

(Pekania pennanti) in fresh snow in winter

n
o
d

Linking questions
i
r

1. What might c ause a species to persist or go extinct?

t
o

a. Explain how adaptations demonstrate the correlation between form

a

and function in plants. (B4.1.8)

f

b. Distinguish, using examples, between top-down and bottom-up

u
x

limiting factors. (C4.1.17)

l

c. O utline two named examples of species extinction including c auses

O

and ecologic al consequences. (A4.2.3)

2. How do species exemplify both continuous and discontinuous patterns

v

of variation?
E

a. With reference to an example, outline what is meant by polygenic

inheritance. (D3.2.14)

b. Distinguish between codominance and incomplete dominance.

(D3.2.9)

c. With reference to a named example, explain the mechanism behind

disruptive natural selection. (D4.1.12)

115
 A3.2 Classic ation and cladistics

What tools are used to classify organisms into taxonomic groups?

s
s
Historic ally, scientists have used shared observable features to

classify groups of organisms. The organism shown in Figure 1 is

e
Relicanthus daphneae. If it looks like a sea anemone, does that make

it one? It is unusually large for an anemone, with tentacles up to

r
7feet long. Across several genes, its DNA sequence is distinct from

y
all other anemones. It is c ategorized as a cnidarian. What features

c an we expect to see if that is the classic ation? Anemones are

l
unique among cnidarians in having aps over their stinging cells.

y
▴ Figure 1

n
How would the discovery of aps aect the classic ation of this

unusualanimal?

O
i
s
How do cladistic methods dier from traditional taxonomic methods?

y
In Figure 2, a marabou stork is waiting for an opportunity to c apture
e
any sh that might be dropped by the crocodile. What are the

p
dierences between birds and reptiles that have led them to be
v

classied as separate classes of vertebrates? Molecular analysis has

established that the bird is more closely related to the crocodile

o
i

than the crocodile is to other reptiles such as snakes and turtles.

n

Other than greater homology of DNA, what other morphologic al

and physiologic al features do birds and crocodiles share? If birds

U

descended from dinosaurs, what prevents birds from being

▴ Figure 2
n

reclassied as reptiles?
o
d

AHL only

A3.2.1 Need for classic ation of organisms

i
r

A3.2.2 Diculties classifying organisms into the traditional hierarchy of taxa

t

A3.2.3 Advantages of classic ation corresponding to evolutionary relationships

o

A3.2.4 Clades as groups of organisms with common ancestry and shared characteristics

A3.2.5 Gradual accumulation of sequence dierences as the basis for estimates of when clades
f

diverged from a common ancestor

x

A3.2.6 Base sequences of genes or amino acid sequences of proteins as the basis for
l

constructing cladograms
O

A3.2.7 Analysing cladograms

a

A3.2.8 Using cladistics to investigate whether the classic ation of groups corresponds to
v

evolutionary relationships

A3.2.9 Classic ation of all organisms into three domains using evidence from rRNA base
E

sequences

116
 Organisms

LHA
A3.2.1 Need for classic ation of organisms

Millions of species have been named and described, and more are discovered

every day. Biologists have accumulated huge amounts of knowledge about these

species. This poses a considerable challenge in terms of information storage and

s
retrieval. To make this easier, biologists have devised systems for classifying life.

Classic ation involves placing organisms in groups according to their traits or

s
evolutionary origins.

e
A hierarchic al system of classic ation has been developed over the last 300

r
years. All organisms are divided into major groups; at present, domains are the

broadest type of group. These large groups are subdivided again and again

y
until we reach the basic level of classic ation—the species. Without this system,

it would be very dicult to identify unknown species. Consider the organism

l
pictured in Figure 3.

n
• It is obviously eukaryotic and an animal, so we immediately know the domain

(eukaryotes) and the kingdom (animals). However, there are over a million

O
possible animal species.

i
• We c an see hair and we would be able to find mammary glands, so we c an

s
deduce that it is one of the 6,500 species of mammal.

y
• Other traits show that it is a member of the C arnivora. This limits the e
possibilities to 270species. ▴ Figure 3 What is this organism?

p
• In a similar way, we c an place the organism in the Mustelid family, which
v

contains about 60 species.

o
i

• It then becomes relatively easy to identify the genus and species: Pekania

pennanti—the fisher.
n

Once we know the name of the species, we c an easily access large amounts of
U

information about this organism and the groups to which it belongs. This is the
n

power of classic ation.

o
d

ATL Thinking skills: Evaluating alternative perspectives

i
r

Are classific ation systems invented or discovered?

t
o

It is natural for humans to arrange things in groups, to

a

make it easier to study them. The process of arranging

f

things in groups is classic ation.

u
x

1. The clouds that we see in the sky appear in an

innite variety of forms. The World Meteorologic al

l
O

Organization has developed a classic ation of

a

clouds. Ten genera are recognized, such as cirrus,

stratus and cumulus. These genera are subdivided

v

into species and then varieties. This classic ation

is worthwhile bec ause it enables more accurate

E

prediction of weather. For example, rainfall is

▴ Figure 4 The 10 genera of clouds

unlikely if the clouds are cumulus. Is this classic ation

invented or discovered?

117
 Unity and diversity
LHA

2. In how many ways c an the oval, triangle and tree branches. They also have mammary glands and

square be classied into two groups, based on fur. Southern ying squirrel foetuses develop in the

their similarities and dierences? Is one of these uterus with a placenta. Sugar glider foetuses develop

classic ations better? in their mother ’s pouch. Which features are most

s
important in assessing the relationship between the

two gliding organisms?

s
e
r
P
▴ Figure 5

y
3. The animals in Figure 6 both have a tail for aiding

l
▴ Figure 6 (le) Southern ying squirrel (Glaucomys volans)

balance and a parachute-like membrane that stretches

y
and (right) sugar glider (Petaurus breviceps)

n
from wrist to ankle that allows them to glide between

O
i
A3.2.2 Diculties classifying organisms into

s
the traditional hierarchy of taxa

y
Any classicatory group is a taxon, for example, “phylum”. The plural is taxa.
e
Assigning organisms to groups is taxonomy. Biologists have developed a hierarchy

p
of taxa with ranks from species up to kingdom. This traditional hierarchy is shown
v

in Figure 7, with two examples. A genus contains one or more species, a family

o
contains one or more genera and so on. Moving up through the hierarchy, the taxa
i

contain larger and larger numbers of species that share fewer and fewer traits.
n

In practice, it c an be dicult to classify organisms according to this hierarchy.

Even when taxonomists agree over which species should be classied together,
U

they oen disagree over what taxonomic rank the grouping should have. One
n

taxonomist might think the traits in a group of species are similar enough to form

a genus; another might think they are dierent enough to be a family.

o
d

i
r

Taxon Grey wolf D ate palm

t
o

a
f

u
x

l
O

Kingdom Animals Plants

v

Phylum Chordates Angiosperms

Class M ammals Monocotyledons

E

Order C arnivores Palmales

F amily C anidae Arec aceae

Genus Canis Phoenix

Species lupus dactylifera

▴ Figure 7 Traditional classic ation in the hierarchy of taxa

118
 Organisms

LHA
Th e s e u n c e r ta i n ti e s a re a re s u l t of th e g ra d u a l di ve rge n c e of s pe c i e s and

B
l a rge r gro u ps ove r ti me. Fo r ex a m pl e, as the s pe c i e s in a ge n u s di ve rge

f ro m e ach o t h e r, th e re will e ve n tu a l l y be s u f fi c i e n t di ve rs i ty fo r th e ge n u s

time
to be divided into tw o or m o re s e p a ra te g e n e ra . As d i ve rg e n c e c o n ti n u e s

ove r th o u s a n ds or e ve n millions of ye a rs , th e s e ge n e ra will become di f fe re n t

A

s
enough to be pl a c e d in di ffe re n t families. The i n s ta n t in time when these

s e p a ra ti o n s should h a p pe n c annot be de te r m i n e d o bj e c ti ve l y. Th i s is c alled

s
▴ Figure 8 E ach line represents a species

th e boundary pa ra d ox and, be c a u s e of it, ta xo n o m i c ra n k i n gs a re inevitably

e
over time. How many genera are there at A

ra th e r a r b i t ra r y.

and at B? How c an you justify your answer?

r
P

y
A3.2.3 Advantages of classic ation

corresponding to evolutionary relationships

l
y

n
Biologists agree that classic ation should mirror the evolutionary origins of

species. Two criteria c an be used to judge whether a classic ation achieves this:

O
• Every organism that has evolved from a common ancestor is included in the

i
same taxonomic group.

s
• In each taxonomic group, all the species are evolved from the same

y
commonancestor. e

p
If these criteria are satised, all members of a taxonomic group will share
v

traits that they have inherited from their common ancestor. Such shared traits
▴ Figure 9 Murina beelzebub was recently

o
are known as synapomorphies. This sharing of traits between members of a
discovered in Vietnam. It is a tube-nosed
i

taxonomic group allows biologists to make predictions based on classic ation. bat, with a mass of only 5 to 6 grams. It
n

Two examples are given here.

C

is aggressive when c aptured, hence the

species name

Species of bat
U

New species of bat are sometimes discovered. Bec ause we know that bats are
n

classied as mammals, we c an immediately make predictions with reasonable

certainty: a new species of bat will have a four-chambered heart, hair, mammary
o
d

glands, a placenta and therefore a navel (belly button), plus many other

mammalian features.
i
r

Species of daodil
t
o

Some types of daodil (Narcissus species) produce galanthamine. This substance

a

has been used as a drug for treatment of Alzheimer ’s disease and is one of a
f

group of compounds c alled alkaloids. There is strong evidence that all species in
u
x

the genus Narcissus evolved from a common ancestor. It is therefore reasonable

to predict that other alkaloids are synthesized by Narcissus species. O ver 80

l
O

dierent alkaloids have now been found in species in the genus, some of which
a

are likely to prove useful as drugs.

v
E

▴ Figure 10 Narcissus poeticus

119
 Unity and diversity
LHA

A3.2.4 Clades as groups of organisms with

common ancestry and shared characteristics

Species c an evolve over time and split to form new species. With some highly

successful species, this has happened repeatedly, so there are now large groups

s
of species all derived from a common ancestor. These groups of species c an be

s
identied based on shared characteristics. A group of organisms evolved from a

common (shared) ancestor is c alled a clade.

e
Clades include all the species alive today, together with the ancestral species.

r
They also include any species that evolved from the common ancestor and then

P
bec ame extinct. Clades c an be very large and include thousands of species, or

y
they c an be very small with just a few species. For example, birds form one large

clade with about 10 thousand living species, bec ause they have all evolved from

l
a common ancestral species. In contrast, the tree Ginkgo biloba is the only living

n
member of a clade that evolved about 270 million years ago. There have been

t
other species in that clade but all are now extinct.

O
i
It is not a l w ays o bv i o u s which species h ave e vo l ve d f ro m a c o m mo n ancestor

s
and should th e re fo re be included in a c l a d e. Th e mo s t o bj e c ti ve evidence

comes f ro m ba s e sequences of ge n e s or amino acid sequences of pro te i n s .

y
Th e genomes of o rga n i s ms e c o n ta i n a huge amount of i n fo r ma ti o n , f ro m which

th e i r e vo l u ti o n a r y h i s to r y c an be deduced. Wh e re s e qu e n c e da ta is not

p
av a i l a b l e, m o r ph o l o g i c a l tra i t s c an be used to a ss i gn o rg a n i s ms to c l a de s .
v

Th i s is p a r ti c u l a r l y useful w i th s pe c i e s that h ave be c o me ex ti n c t, w h e re

o
s e qu e n c e da ta is not av a i l a b l e and the only evidence c o me s f ro m fo ss i l s .
i

Every species is in multiple clades, not just one. Smaller clades are “nested”
n

within larger clades. For example, Figure 11 shows 10 species of gymnosperm

(non-owering seed plants). Araucaria araucana (the monkey puzzle tree) is in

U

a clade with Podocarpus totara bec ause they have a common ancestor. They
n

are nested in a clade with Taxus baccata and the two species below it in the

tree diagram. Those ve species are nested in a clade with Pinus radiata and
o
d

the three species below it—again bec ause of common ancestry. Finally, those

9 species plus Gingko biloba are in a clade that includes all 10 of these species,
i

plus all other gymnosperms.

r

t
o

Taxus baccata (yew)

a
f

Cephalotaxus fortunei
u
x

Cupressus sempervirens (cypress)

l

Araucaria araucana (monkey puzzle)

O

Podocarpus totara
v

Pinus radiata (Monterey pine)

E

Ephedra sinica

Welwitschia mirabilis

Gnetum africanum

Ginkgo biloba

▴ Figure 11 Smaller clades are nested within larger ones

120
 Organisms

LHA
Paradigm shis

A xed ranking of taxa (kingdom, phylum and so

Taxon Grey wolf Taxon D ate palm

on) is arbitrary as it does not reect the gradation

Kingdom Animals Kingdom Plants

s
of variation. Cladistics oers an alternative

approach to classication using unranked Clade ParaHoxozoa Clade Tracheophytes

s
clades. This is an example of a paradigm shi in
Clade Bilateria Clade Angiosperms

e
scientic thinking.

Clade Nephrozoa Clade Monocotyledons

Increasingly, clades are being named and

Clade Deuterostomia Clade Commelinids

r
used in classic ation instead of the ranks in

Clade Chordata Order Arec ales

the traditional hierarchy of taxa. Figure12

y
shows how date palms and grey wolves
Clade Olfactores F amily Arec aceae

have been classied using clades. The taxa

Clade Vertebrata Genus Phoenix

l
from species up to order, and the kingdom,

n
Clade Tetrapoda Species dactylifera

are still assigned using traditional taxa. The

Clade Amniota
intermediate levels in the hierarchy are all

O
referred to as clades and the number of levels
Class M ammals

i
is not xed.

Order C arnivores

s
1. What is the advantage of this approach to
F amily C anidae

y
classic ation?

Genus Canis
e
2. What makes this a paradigm shi rather
Species lupus

p
than a modic ation?
v

▴ Figure 12 Classic ation using clades

o
i
n

A3.2.5 Gradual accumulation of sequence

dierences as the basis for estimates of when

U

clades diverged from a common ancestor

n

Dierences in the base sequence of DNA—and therefore in the amino acid

o
d

sequence of proteins—are the result of mutations. These dierences accumulate

gradually over long periods of time. If we assume that this happens at a roughly
human chimpanzee bonobo
i

constant rate, we c an use the number of dierences to estimate the time since
r

two species diverged from a common ancestor. This method of estimating time is
o

known as the “molecular clock”. The larger the number of sequence dierences
a

between two species, the longer since they diverged from a common ancestor.
1 Myr ago
f

When considering timings based on the molecular clock, it is important to

x

remember the assumption that has been made—that mutations accumulate

l

at a constant rate. In fact, this rate c an vary and is aected by the length of the
O

generation time, the size of the population, the intensity of selective pressure and

other factors. Thus, the molecular clock c an only give estimates.

v

Base sequence dierences have been used to estimate when humans split from

4.5 Myr ago

−9 −1

the nearest living relatives. Based on a mutation rate of 10 yr , this happened

E

4.5million years ago. Using the same assumptions, common chimpanzees and

bonobos split more recently—around one million years ago. It is also possible to

estimate when humans split from other hominid species and therefore when the ▴ Figure 13 Estimated dates for the

divergence of humans and chimpanzees,

most recent common ancestor of all humans existed. Using variations in the base

based on the base sequences of the entire

sequence of mitochondrial DNA as a molecular clock, our most recent common

genomes
ancestor is estimated to have lived 150,000 years ago.

121
 Unity and diversity
LHA

Applying technology to process data: Conducting a sequence alignment

Sequence similarities in the DNA or proteins from dierent Various web-based applic ations c an be used to c arry

organisms suggest evolutionary relationships. The greater out sequence alignment, such as the Multiple Sequence

the similarity, the closer the relationship. It is possible to Alignment tools found at the European Bioinformatics

s
compare two relatively short sequences visually. However, Institute (EMBL-EBI). In addition, the BLAST search web

s
comparison of longer sequences or multiple sequences page of the National Centre of Biotechnology Information

relies on the use of computer algorithms. (NCBI) will align two sequences. Figure 14 shows a

e
DNA sequence alignment of nine dierent organisms,

r
generated using the programme ClustalX.

y
l
y

n
t

O
i
s
▴ Figure 14 A DNA sequence alignment of the cytochrome oxidase gene for four dierent large c ats, generated using the

r
programme ClustalW

y
e
The NCBI website (http://www.ncbi.nlm.nih.gov/) has tools for c arrying

p
out a comparison of protein and DNA sequences. In this example, we
v

will conduct a sequence alignment using the cytochrome oxidase (cox1)

protein for two species of primate

o
c alled tarsiers. Horseld’s tarsier, variously
i

classied as Cephalopachus bancanus and Tarsius bancanus, is a threatened

n

species that lives in Borneo and Sumatra. The cox1 sequence for this tarsier

will be compared with the sequence of the same gene for the Philippine
U

tarsier (Carlito syrichta). There is some uncertainty over the classic ation of
n

Horseld’s tarsier and sequence comparison is oen used to resolve this kind

of controversy. Use the search term cytochrome c oxidase subunit I [Tarsius

banc anus]. Click on the COX1 highlighted text to determine the accession
o
d

numbers (They start with NC_ for DNA and NP_ for proteins). Repeat the

procedure using the search term cytochrome c oxidase subunit I [C arlito

i
r

syrichta]. Then go to the BLAST tool (https://blast.ncbi.nlm.nih.gov/) and

t
o

decide whether you are going to align the DNA or protein sequences. Be sure
a

to check the “align two or more sequences”. Identify the dierences in the
f

protein and DNA sequences. Explain how such information c an be used to

u

determine evolutionary relationships.

x

l
O

a
v
E

▴ Figure 17
▴ Figure 15 Horseld’s tarsier ▴ Figure 16 Philippine tarsier

122
 Organisms

LHA
A3.2.6 Base sequences of genes or amino

acid sequences of proteins as the basis for

constructing cladograms

s
Within a clade, some species will be more closely related than others, bec ause

they diverged relatively recently. They will have fewer dierences in base or

s
amino acid sequence. Conversely, species that diverged a longer time ago are

e
likely to have more dierences. By comparing base sequences, it is possible to

estimate how long ago pairs of species diverged. These estimates c an then be

r
used to suggest the order in which the divergences occurred.

y
Much more sophistic ated analysis c an be done using computer soware.

Sequences for all species in a clade c an be compared in combination. The

l
soware c an then use c alculations to determine how the species could have

n
evolved with the smallest number of sequence changes. This is known as the

parsimony criterion. It does not prove how a clade evolved but it indic ates the

t
most probable pattern of divergence.

O
i
Sequence analysis is used to construct a cladogram. A cladogram is a branching

s
diagram that represents ancestor–descendant relationships. An example is

r
shown in Figure 18.

y
European
e

p
Japanese
v

African

o
i
n

Common chimpanzee

Pygmy chimpanzee (bonobo)

U

Gorilla

Orang-utan
o
d

▴ Figure 18 A cladogram for humans and primates

i
r

▴ Figure 19 Which of these three

t

members of the family Hominidae are most

o

Sequence data for more than one gene c an be used to produce multiple
closely related, according to the cladogram
a

cladograms for a group of organisms. If the cladograms show the same pattern of
in Figure 18?
f

divergence, this is strong evidence of how the group evolved.

u
x

Applying technology to process data: Using soware to construct a

l
O

phylogenetic tree
v

A phylogenetic tree created using the methods of are more likely to be related than Afric an c ats are to North

cladistics is a cladogram. A hypothesis about evolutionary Americ an c ats.

E

relationships c an be tested using bioinformatics soware.

Follow these steps to construct a cladogram:

For example, consider large c ats from around the world.

a. Search a database to nd DNA sequences for a gene

Their evolutionary relationship is likely to be correlated

which is conserved across many species such as

with their current geographic distribution. More closely

cytochrome c oxidase subunit 1. The National Center

related c ats are more likely to be closer to each other in

for Biotechnology Information site (NCBI) is freely

geographic distribution. For example, Afric an large c ats

searchable and is recommended. We are going

123
 Unity and diversity
LHA

to construct a phylogenetic tree for the following g. Edit the titles but remember to include the ‘>’ symbol

species: puma (Puma concolor), tiger (Panthera tigris), and to separate words in the title with an underscore.

snow leopard (Panthera uncia), lion (Panthera leo) For example: >Panthera_uncia

and leopard (Panthera pardus).

h. Collate all of the DNA sequences representing the

s
b. Search the NCBI website for the DNA sequences dierent organisms in the study. Depending on the

using the search term: cytochrome c oxidase subunitI soware to be used in later steps, the sequences

s
[Genus species] for example cytochrome c oxidase could be copied and pasted into a text le. In

e
subunit I [Panthera leo]. this example, you will use the Multiple Sequence

Alignment tool (Clustal Omega found at the EMBL

c. Under the Genomic regions, transcripts and

r
website).
products, choose ‘FASTA’ which should display

a nucleotide sequence. Highlight all of the i. Upload the le to Clustal Omega.

y
DNA sequence including the title (for example
j. Perform the sequence alignment. Through

‘>NC_010638.1:6099-7643 Panthera uncia)

observation c an you determine the relationship

l
y
d. Open either Notepad from your PC or TextEdit between the c ats?

n
on a M ac.
k. Construct the tree using Clustal Omega.

t
e. Paste your sequence into the text editing document.
l. Compare your tree to other trees available through an

O
i
f. Repeat with several other sequences from dierent internet search. How does your tree compare?

s
organisms.

y
e

p
Hypotheses: Parsimony as a criterion for judgement
v

A cladogram is a statement of hypothesized evolutionary Sequences could have reached their current order in many

relationships. Dierent criteria for judgement c an lead

o
dierent ways. For example, the base cytosine could change
i

to dierent hypotheses. Parsimony analysis is used to to thymine, then back to cytosine and then to thymine
n

select the most probable cladogram, in which observed again. In this case, parsimony analysis would presume that

sequence variation between clades is accounted for with the change was simply cytosine to thymine. The tree that
U

the smallest number of sequence changes. involves the smallest number of evolutionary changes is
n

chosen: although there is no proof of how the clade actually

evolved, the simplest explanation is most likely to be true.

o
d

locus

taxon

1 2
i
r

T
t
o

II G T
a

A C
III
f

IV G T
x

l
O

II IV I III II III IV I I II III IV

v
E

two changes three changes three changes

▴ Figure 20 Cladograms showing DNA base changes: What base was present at locus 1 in the

ancestor? At locus 2? Which cladogram is the best one if parsimony is the criterion for judgement?

124
 Organisms

LHA
A3.2.7 Analysing cladograms

When analysing cladograms, remember:

• A cladogram is a tree diagram with a number of branches.

s
• The terminal branches are ends that represent individual clades. These may

be species or groups of species that are not subdivided on the cladogram.

s
• The branching points on a cladogram are c alled nodes. Usually, two

e
clades branch off at a node but sometimes there are three or more. A node

represents the point at which a hypothetic al ancestral species split to form

r
two or more clades.

y
• Two clades that are linked at a node are relatively closely related. Clades that

are only connected via a series of nodes are less closely related.

l
• The root is the base of the cladogram. This is the hypothetic al common

n
ancestor of all the clades.

t
• Some cladograms include numbers to indic ate numbers of sequence

O
differences.

i
s
• Some cladograms are drawn to sc ale, based on estimates of the time since

each split occurred.

y
• The pattern of branching in a cladogram is assumed to match phylogeny of
e
the organisms—the evolutionary origins of each species.

p
v

Although cladograms c an provide strong evidence for the evolutionary history

of a group, they c annot be regarded as proof. Cladograms are constructed on

o
i

the assumption that the smallest possible number of mutations occurred that c an
n

account for current base or amino acid sequence dierences. Sometimes this

assumption is incorrect and pathways of evolution were more convoluted. It is

U

therefore important to be c autious when analysing cladograms. Where possible,

n

you should compare several versions that have been produced independently

using dierent genes.

o
d

A B C D E F G H I J
i
r

t
o

nodes
a

terminal branches
f

u
x

internal branches
l
O

a
v

root

▴ Figure 21 Cladograms usually show only two branches forming at each node.
E

Occ asionally three or more branches are shown, as on the right of this diagram.

With more research it would almost certainly be found that either H, I or J split o

rst, followed later by a split between the other two species

125
 Unity and diversity
LHA

Data-based questions: Origins of turtles and lizards

Cladograms based on morphology suggest that turtles 1. Deduce, using evidence from the cladogram,

and lizards are not a clade. To test this hypothesis, whether humans are more closely related to the short-

s
microRNA genes have been compared for nine species tailed opossum or to the duck-billed platypus. [2]

of chordate. The results were used to construct the

2. C alculate how many microRNA genes are found in

s
cladogram in Figure 22. The numbers on the cladogram
the mammal clade on the cladogram but not in the

show which microRNA genes are shared by members of

e
other clades. [2]

a clade but not by members of other clades. For example,

3. Discuss whether the evidence in the cladogram

r
there are six microRNA genes that are found in humans
supports the hypothesis that turtles and lizards

and short-tailed opossums but not in any of the other

are not a clade. [3]

y
chordates on the cladogram.

4. Evaluate the traditional classic ation of tetrapod

chordates into amphibians, reptiles, birds and

l
mammals using evidence from the cladogram. [3]

n
African clawed frog

O
i
s
r
731

11

88

167

176

043

y
short-tailed opossum
3
e
378

0

681

p
v

duck-billed platypus

o
i
n

1 ebra finch
731

04

46

4

131

3081

871

4871

1871

71

671

4471

3471

71

661

1461

761

1

7641

0641

141
1
chicken
U
171

alligator

1
o
d
7761

painted turtle
i
r

4
t
33

3

13

03
o

liard
a
f

▴ Figure 22
u
x

l
O

A3.2.8 Using cladistics to investigate

whether the classic ation of groups

v

corresponds to evolutionary relationships

E

Since the 1990s, it has been relatively easy to nd the base sequences of genes

or even whole genomes. This sequence data has allowed researchers to check

traditional classic ations of plants and animals, using the objective method

of cladistic analysis. In many c ases, cladistics research has conrmed that the

traditional classic ation matches the most probable pathways of evolution.

126
 Organisms

LHA
In some c ases, however, the species placed in a taxonomic group do not all

share a common ancestor. In other c ases, species that have evolved from the

same common ancestor have been placed in dierent groups. In such c ases,

reclassic ation is justied. The following c ase study illustrates this process. The

details are not important but they will help you to understand the principles

s
involved. You could study the reclassic ation of other groups, such as the

Sterculiaceae, if you wish to nd out more.

s
e
Reclassic ation based on cladistic analysis

There are more than 400 families of angiosperms (owering plants). Until recently, the eighth largest was the

r
Scrophulariaceae, commonly known as the gwort family. It included over 275genera, with more than 5,000 species.

P
Taxonomists used cladistics to investigate the evolutionary origins of the gwort family. They found that species in this

y
family did not share a single common ancestor so were not a true clade.

l
A major reclassic ation was c arried out. Five groups of species were moved to other families, leaving fewer than half

n
of the original species in the gwort family. It is now only the 36th largest among the angiosperms. A summary of the

changes is shown in Figure 23.

O
Two small families were merged

i
with the figwort family

s
the buddlea family, uddleaceae

and the myoporum family, yoporaceae

y
e

p
v

o
i

Two genera were moved to

Nearly 50 genera have
n

a newly created family,

been moved to the

Scrophulariaceae
the calceolaria family,
plantain family,
U

(The figwort
Calceolariaceae
Plantaginaceae

family)
n
o
d

i
r

t
o

Thirteen genera have been About  genera of

a

transferred to a newly created parasitic plants have been

f

family, the lindernia family, moved to the broomrape

u
x

Linderniaceae family, robanchaceae

l

▴ Figure 23
O

a
v
E

▴ Figure 25 Veronica beccabunga

▴ Figure 24 Scrophularia chrysantha (golden

(European speedwell) has been transferred to the

gwort) has remained in the gwort family

Plantaginaceae (plantain family)

127
 Unity and diversity
LHA

Data-based questions: Mustelid classic ation

The Mustelidae is a family of 59 species of mammal, 1. The nodes on the cladogram have been numbered.

classied into 22 genera on the basis of morphology. What is indic ated by a node? [2]

s
Base sequences of 22 gene segments were analysed to
2. The sc ale bar shows how many base substitutions are

produce thousands of dierent hypothetical cladograms.

indic ated by each length of horizontal line. What c an

s
Figure 26 shows the consensus cladogram, based on
be estimated from the number of base substitutions

maximum parsimony. Bassariscus astutus and Procyon

e
since two species diverged? [2]

lotor, at the bottom of the cladogram, are members of a

3. Using evidence from the cladogram, discuss whether:

r
dierent family and were used for reference purposes.

Such species in a cladogram are called the outgroup. All a. Martes pennanti should be moved to a dierent

y
the other species from Aonyx capensis to Taxidea taxus are genus [2]

members of the Mustelidae. According to the traditional

b. the Mustelinae should be subdivided into seven

l
classication, the Mustelidae family is subdivided into the

smaller groups [2]

n
Lutrinae and Mustelinae. A further proposed subdividsion

c. Bassariscus astutus and Procyon lotor should be

is shown to the right of the cladogram. There is evidence

t
moved to the Mustelidae family. [2]
in the cladogram to suggest that some species should be

O
i
moved to a dierent genus.

s
r

y
e

p
v

o
i
n

C
U

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

▴ Figure 26

128
 Organisms

LHA
F alsic ation: Reclassic ation based on phylogeny

A cladogram depicts a hypothesized evolutionary relationship.

Bec ause scientic knowledge claims are based on empiric al

s
evidence, it is not possible to claim with absolute certainty

that they are true. Certainty becomes possible if we c an nd a

s
counterexample and establish what is not the c ase. K arl Popper

e
c alled this property of scientic knowledge claims “falsiability”.

Hypotheses, theories and other scientic knowledge claims may

r
eventually be falsied.

Elephant shrews are small insect-eating mammals native to Afric a.

y
Their common English name, elephant shrew, comes from a

perceived likeness between their long noses and the trunk of an

l
elephant, and their supercial similarity with shrews. Phylogenetic

n
analysis has shown that elephant shrews should not be classied as
▴ Figure 27 E ast Afric an black and rufous elephant

true shrews; in fact, they are more closely related to elephants than

t
shrew or Sengi (Rhynchocyon petersi)

O
to shrews!

i
s
r

y
A3.2.9 Classic ation of all organisms into
e

p
three domains using evidence from rRNA
v

base sequences

o
i

Traditional classic ation systems have recognized two major c ategories of

n

organisms based on cell types: eukaryotes and prokaryotes. This classic ation

is now regarded as inappropriate bec ause the prokaryotes are so diverse. In

U

particular, when the base sequences of ribosomal RNA were determined, it

n

bec ame apparent that there are two distinct groups of prokaryotes. They were

given the names Eubacteria and Archaea.

o
d

Most classic ation systems therefore now recognize three major c ategories

of organism, Eubacteria, Archaea and Eukaryota. These c ategories are c alled

i
r

domains, with all organisms classied into the three domains. Members of the
t

domains are usually referred to as bacteria, archaeans and eukaryotes. Bacteria

o

and eukaryotes are relatively familiar to most biologists but archaeans are oen
a

less well-known.
f

Bacteria Archaea Eukaryota

x

Green filamentous
l

Slime
bacteria
O

Animals
moulds
a

Spirochetes

Gram
Fungi
Methanobacterium Halophiles

Proteobacteria
positives
Methanococcus
v

Plants

Cyanobacteria Ciliates
E

Flagellates

◂ Figure 28 Tree diagram showing

relationships between living organisms

based on base sequences of ribosomal RNA

129
 Unity and diversity
LHA

ATL Social skills: Actively considering the perspective of others

During debates, you may nd yourself disagreeing with Approach conversations with the understanding that you

someone. If this happens, take time to be fair-minded might be mistaken and that other people might have valid

s
and consider other people’s perspective. Be sure that ideas. The consensus is that classication should be based

you are not using dierent criteria for judgement. For on evolutionary relationships, as this allows us to make

s
example, it is possible to argue that the elephant shrew predictions. For example, two closely related organisms

and tree shrews are not related, or that they are related, should have similar metabolism. However, in some

e
depending on your criteria for judgement. contexts it is also reasonable to classify an organism by its

r
niche. In this case, the elephant shrew could be considered

related to other shrews as they are all insectivores.

y
l
y

n
Data-based questions: Similarities and dierences in microbial cell wall structure

t
Figure 29 shows the plasma membrane and cell wall structures in ve groups of microorganism.

O
i
1. Compare the plasma membranes of the microorganisms. [2]

s
2. Compare the cell walls of the microorganisms. [2]

3. Distinguish between the cell wall of Group Z and the other groups. [2]

y
4. a. Compare and contrast the structures outside the cell wall in Groups V, W, X and Y. [4]
e
b. Construct a cladogram based on these comparisons and contrasts. [4]

p
5. Deduce which of the ve groups is the fungi. [1]
v

o
i
n

C
U

lipopoly-
n

saccharide

outer
o
d

membrane

cell wall
i
r

plasma
t

membrane
o

V W X Y Z
f

u
x

highly variable amino sugar mannose

l
O

D-alanine arabinose
N-acetylmuramic acid
a

ribitol phosphate
N-acetylglucosamine arabinogalactan
v

glycerol phosphate
phosphate
proteins
E

N-acetylmannosamine

glucose

▴ Figure 29

Source: Chen, Y., Fischbach, M. & Belkaid, Y. Skin microbiota–host interactions.

Nature 553, 427–436 (2018). https://doi.org/10.1038/nature25177

130
 Organisms

Linking questions

1. How c an similarities between distantly related organisms be explained?

a. Outline the concept of an ecologic al niche. (B4.2)

s
b. Describe the mechanism of evolution by natural selection. (D4.1)

s
c. Explain the mechanism of convergent evolution. (A4.1.5)

e
2. What are some examples of ideas over which biologists disagree?

r
a. Describe the evidence that conrmed DNA and not protein was the

genetic material. (A1.2.14)

y
b. Explain how using the principle of parsimony could lead to an error in

l
classic ation. (A3.2.6)

n
c. Suggest why c ategorization of some populations as “evolutionarily

distinct” and therefore a higher priority for conservation might be

O
controversial. (A4.2.8)

i
s
r

y
e

p
v

o
i
n

C
U

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

131
 Unity and diversity

TOK

How does the way in which we organize or

s
s
classify knowledge aect what we know?

e
Perception is the act of interpreting sensory information. The N atural classic ation looks at evolutionary relationships.

r
environment presents you with endless sensory information, Thus, the lynx and the musk de er are groupe d together

most of which you ignore as unimportant. What you do as placental mammals, while the spotte d-taile d quoll (a

y
notice, you classify in a variety of ways—oen without even marsupial that occupies the niche of a small c at) and the

realizing it. For example: When you hear a loud sound, you whiptail w allaby are groupe d together as marsupials.

l
might classify it as representing a threat or not a threat; or In terms of trophic level, the de er and the w allaby are

n
you might identify the direction from which it c ame. When groupe d together be c ause they are both herbivores. In

you see a fruit on a plant, you might classify it as ripe or not, terms of habitat, the quoll and the lynx are both

O
or edible or not. In everyday language, you might classify forest dwellers.

i
organisms as domestic ated or wild; dangerous or harmless;

The names used c an impact our perception, bec ause

s
and so on. There are innite ways to interpret and organize

dierent names predispose the listener to focus on a

your observations.

y
particular aspect of the organism. This is particularly

Similarly, scientists classify organisms in a number of ways. apparent in folk taxonomy—the everyday names given to
e

p
For example, they might group them by morphology things. For example, insects in the family Pentatomidae

(physic al similarity to other organisms), phylogeny have a shape which looks like a heraldic shield when
v

(evolutionary history) or niche (ecologic al role). viewed from above. This is why, in some folk taxonomies,

o
i

they are referred to as “shield bugs”. Bec ause they release

Consider the four animals in Figure 1. They c an be classied

a strong-smelling spray when threatened, they are referred

n

by trophic level; marsupial or placental; niche or habitat;

to in other folk taxonomies as “stink bugs”. The L atin family

patterned fur or monochrome; conservation status

name, Pentatomidae, refers to the fact that their antennae

U

(threatened or not); and so on. E ach c ategorization focuses

have ve segments.

n

on a dierent feature or features of the organism.

o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

▸ Figure 1 A Siberian musk deer (top le);

a lynx (top right); a whiptail wallaby (bottom

le) and a spotted-tailed quoll (bottom right)

132
 Organisms

The Cerion snail is endemic to the Caribbean. Folk taxonomies refer

to it as the peanut snail or the honeycomb snail. Figure 3 shows

some of the varieties of snail from the three islands of the Netherlands

Antilles. Nineteenth century naturalists classied Cerion snails into a

large number of dierent species based on physical dierences (such

s
as colour, lip thickness and number of grooves). In the 20thcentury,

molecular biologists were able to show that the variety represented

s
a much smaller number of species. All of the snails shown in Figure

e
3 belong to the species Cerion uva. The environment has an impact

on gene expression and how the snails develop. On windy, wavy

r
shores, the snails develop thicker and stronger shells. On low energy

coastlines, colour dierences are more pronounced.

y
Taxonomists are scientists who classify organisms. Taxonomists

l
themselves c an be classied! “Lumpers” are those who tend to

n
see dierent individuals as varieties of the same species. “Splitters”

are more prone to emphasize these dierences as indic ative of

t
uniquespecies.

O
i
▴ Figure 2 A shield bug or stink bug

s
r

y
e

p
v

o
i
n

C
U

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

▴ Figure 3 Cerion uva snails

133
 Unity and diversity

End of chapter questions

1. Evidence suggests that humans are descended from c. C anine teeth c an be divided into two groups, large

a species of Afric an ape that has spread to colonize or small. The evidence from c anine teeth supports

s
new areas. The species most closely related to Model C. Gorillas have large teeth. Deduce the

s
humans are the chimpanzee and the gorilla. Studies type of teeth that chimpanzees and humans have.

of biochemistry and chromosome numbers provide

d. Humans, chimpanzees and gorillas all possess

e
conflicting evidence of the evolutionary relationship

broad flat molar teeth for grinding plant matter.

between these three primates. Three models showing

r
Lion molars are not adapted for grinding. Suggest

possible relationships are shown in Figure 1. Some of

why eating plant matter requires molar teeth while

P
the evidence on which the diagrams were constructed

y
meat eating is less reliant on broad, flat molars. [2]

is shown in Table 1.

e. O utline the evidence from chromosome 2

l
a. Identify which model appears correct, based on the

of the relatedness of humans, gorillas

n
evidence from chromosome number. [1]

and chimpanzees. [3]

t
b. Evaluate each of the models according to the

O
biochemic al evidence. [3]

i
s
Model A Model B Model C

y
H G C H C G H G C
e
Key

p
CA common ancestor
v

H human

o G gorilla
i

C chimpanzee
n

CA CA CA
U

▴ Figure 1
n

Evidence Human Chimpanzee Gorilla

o
d

Chromosome number 46 48 48

Plasma proteins same as gorilla and same as human and gorilla same as human and chimpanzee
i
r

chimpanzee
t
o

Myoglobin diers from chimpanzee and same as gorilla same as chimpanzee

a

gorilla by one amino acid

f

Haemoglobin same as chimpanzee same as human diers from human and

u
x

chimpanzee by one amino acid

l

▴ Table 1
O

a
v
E

134
 Organisms

2. One method used by microbiologists to distinguish between Archaea and

Eubacteria is based on the conditions they need for survival. Both groups include

thermophiles—species that are adapted to live at high temperatures. The graph

in Figure 2 shows the optimum temperature and minimum pH required for

growth by selected species of Archaea and thermophilic Eubacteria.

s
s
110
C°

e
/

100
erutarepmet htworg mumitpO

r
P
90

y
l
80

n
70

O
i
60

s
r

y
50

0 1 2 3 4 5 6 7 8
e

p
Minimum pH supporting growth
v

o
e rhaea thermophii uateria
i

oure apte rom   aentine 2007 ‘aptations to energ stress itate the eoog an
n

▴ Figure 2
U

a. State the highest optimum growth temperature recorded for the

thermophilic Eubacteria. [1]

o
d

b. State the relationship between minimum pH supporting growth and

i
r

optimum growth temperature for Archaea. [1]

t

c. Compare the results for the Archaea with those for the thermophilic
o

Eubacteria. [2]
f

d. Wi th re fe re n c e to the data, s u g ge s t w hy th i s method would

u
x

not a l w ays be suitable fo r d i s ti n g u i s h i n g between A rc h a e a and

th e r m o p h i l i c E u ba c t e r i a . [2]
l
O

e. State a possible habitat for methanogenic Archaea. [1]

a
v
E

135
 Unity and

s
d i v e rs i t y

s
e
r
4 Ecosystems

y
l
Analogous and homologous structures exemplify the

n
theme of unity and diversity. Both patterns arise due to the

t
selection pressures within an ecosystem. Biotic and abiotic

O
i
factors provide the pressures that contribute both to natural

s
selection and to species diversic ation. The structure–

y
function relationship
e exists bec ause natural selection

favours individuals that are adapted to their environment.

p
O ver generations, the characteristics of those members of
v

o
the population that survive to reproductive age become
i

more common. The change in species over time is known

n

as evolution. When unrelated species encounter the same

selection pressures, they can develop analogous structures

U

that are similar in appearance and function but have dierent

n

histories. For example, the long-eared jerboa (Euchoreutes

o

naso) and kangaroos have distinct evolutionary histories.

d

However, they have both developed long ears for heat

i
r

exchange, movement by hopping and an extended tail

t
o

for balance. These features are an example of convergent

a

evolution, a result of both organisms living in arid habitats.

f

Yet, they have signicantly dierent reproductive strategies

x

as the jerboa develops a placenta during pregnancy and the

l
O

kangaroo is a marsupial which means its young complete

a

development in a pouch outside of the uterus. These

v

examples show that the habitat of an organism can drive both

convergence and divergence. It follows that loss of habitat

E

and unique environments is a signicant factor increasing the

threat of extinction of species. Biodiversity is the variety of life

in all its forms, levels and combinations, including ecosystem

diversity, species diversity and genetic diversity.

A4.1 Evolution and speciation

s
What is the evidence for evolution?

s
The theory that species change over time by the

e
mechanism of natural selection has such strong

predictive and explanatory power that it is unlikely

r
to be falsied. Figure 1 shows both fossil and human

pentadactyl limb evolution. The ve-ngered

y
pentadactyl hand is shared by humans with ancestors

going back over 300 million years of evolution. Here,

l
a human hand is shown with the foot bones of a small

n
predatory North Americ an Permian reptile c alled

C aptorhinus, which is approximately 280 million years

O
old. Explain how the shared anatomy of limbs with

i
diverse functions provides evidence forevolution.

s
◂ Figure 1

y
e

p
How do analogous and homologous structures exemplify commonality and diversity?
v

The wings of a bat and a seagull are similar in form and function.
o
i

If this is not a result of common ancestry, how did these

n

analogous structures develop? What is the role of selection

pressures in evolution? What is the distinction between

U

analogous and homologous structures?

n

Why do organisms with a common ancestry that are subjected

to dierent selection pressures become increasingly dierent?

o
d

How do homologous structures provide evidence of evolution?

Are the hands of a human and bonobo ape ( Pan paniscus)

i
r

homologous or analogous structures? What is the signic ance of

t

▴ Figure 2
the opposable thumb to evolution?
o

a
f

SL and HL AHL only

u
x

A4.1.1 Evolution as change in the heritable characteristics of A4.1.8 Dierences and similarities between sympatric and

a population allopatric speciation

l
O

A4.1.2 Evidence for evolution from base sequences in DNA A4.1.9 Adaptive radiation as a source of biodiversity
a

or RNA and amino acid sequences in proteins A4.1.10 Barriers to hybridization and sterility of interspecic

A4.1.3 Evidence for evolution from selective breeding of hybrids as means of preventing the mixing of alleles
v

domestic ated animals and crop plants between species

A4.1.4 Evidence for evolution from homologous structures A4.1.11 Abrupt speciation in plants by hybridization and
E

A4.1.5 Convergent evolution as the origin of analogous polyploidy

structures

A4.1.6 Speciation by splitting of pre-existing species

A4.1.7 Roles of reproductive isolation and dierential

selection in speciation

137
 Unity and diversity

A4.1.1 Evolution as change in the heritable

characteristics of a population

There is strong evidence for the characteristics of populations changing over

time. Biologists c all this process evolution. It is how the diversity of life developed

s
and lies at the heart of a scientic understanding of the natural world. Evolution

s
only concerns heritable characteristics—traits that are inherited by ospring from

parents. This is emphasized in the denition:

e
Evolution is change in the heritable characteristics of a population.

r
The mechanism of evolution is now well understood—it is natural selection

y
(explained in Topic D4.1). Evolution by natural selection is also c alled D arwinism.

l
There is also strong evidence for the characteristics of individual organisms

y
changing during their lifetimes. For example:

n
• trees c an develop a very asymmetric form if they grow in a position exposed

t
to wind

O
i
• birds are inuenced by hearing their parents singing when they develop their

s
song

y
• human tennis players develop stronger muscles and bones in the arm they

use to hold the racket

e

p
• children learn the languages their parents speak.
v

o
These are known as acquired characteristics.
i

Before Charles D arwin published On the Origin of Species in 1859, the leading
n

theory for evolution was based on inheritance of acquired characteristics. The

main proponent of this theory was Jean-Baptiste L amarck, so it is known as

U

L amarckism. It is obvious that seeds from a tree growing asymmetric ally will not
n

grow into asymmetric ospring unless they are exposed to the same environment

as the parent. Similarly, a tennis player ’s children will not develop stronger
o
d

bones in one arm than the other. No mechanism has been discovered for the

environment c ausing specic adaptive changes to the base sequence of genes,

i

or for it c ausing the creation of new genes. Therefore, acquired characteristics are
r

not inherited and do not lead to evolution. L amarckism has been falsied again
▴ Figure 3 Windswept hawthorn trees on
o

and again, despite repeated attempts to revive the theory.

a Welsh hilltop
a
f

Theories: Pragmatic truth

x

In everyday language, a “true” statement is one that The theory of evolution by natural selection predicts
O

everyone agrees corresponds to reality. However, the and explains a broad range of observations, such as
a

correspondence theory of truth is not the only possibility. antibiotic and pesticide resistance and also the existence
v

For example, the pragmatic theory of truth holds an of homologous and analogous structures. Thus the theory

assertion to be true if it “works”. is unlikely to be falsied. However, the nature of science

E

makes it impossible to prove formally that the theory of

Knowledge claims in science are based on observations of

evolution by natural selection is true. It is a pragmatic

a fraction of possible cases or instances. Scientists use their

truth and is therefore regarded as a theory, despite all the

observations to form generalizations that are then tested.

supporting evidence.
If the generalizations are supported, a theory emerges. If

the theory can explain and predict future observations, it is

said to be a pragmatic truth: a truth that works.

138
 Ecosystems

A4.1.2 Evidence for evolution from base

sequences in DNA or RNA and amino acid

sequences in proteins

s
If evolution is a change in the heritable characteristics of a population, we c an

expect to see changes in genes whenever evolution occurs. These changes will

s
happen in the base sequence of DNA or RNA and in the amino acid sequences

e
of proteins made using those base sequences. Consider the evolution of the

coronavirus that c aused a pandemic starting in 2020 (COVID-19). M any base

r
sequence changes occurred in the genes of this coronavirus, aecting the viral

traits. Some new variants were more successful than earlier ones in spreading

y
through the human population—the virus evolved.

l
Evidence for evolution also comes from comparing base sequences of the same

n
gene in dierent species. A clear relationship is seen: the more closely related

two species are, in their morphology and other traits, the fewer dierences in

t
base sequence there are. This trend is dicult to explain without evolution. It is

O
i
convincingly explained by the theory that species develop over time, gradually

s
diverging from a common ancestor as a result of dierences in natural selection.

r
In addition, observed combinations of dierences are only easily accounted for

y
by repeated splitting of ancestral species by evolution. This is why cladograms
e
based on sequence dierences usually match closely with classic ations based

p
on morphology and the likely sequence of splits between lineages.
v

o
Evidence of evolution also comes from gene families that occur across diverse
i

groups of organisms. For example, the Hox gene family occurs widely in
n

animal genomes. Genes in this family help to determine the body plan during

development. Similarities between Hox genes c an only reasonably be explained

U

by common ancestry, with duplic ation to give multiple copies of the gene and

gradual modic ation for dierent functions in dierent lineages. Hox genes occur
n

in cnidaria and in all animals with a clear head-to-tail axis, including annelids,

arthropods and vertebrates; these species form a clade known as the bilateria.
o
d

i
r

t
o

a
f

u
x

l
O

a
v

lab pb Dfd Scr Antp Ubx Abd-A Abd-B

E

▴ Figure 4 The fruit y Drosophila has eight Hox genes which help to organize head-to-

tail development of dierent parts of the body. Humans have 39 Hox genes which help to

organize our head-to-tail development

139
 Unity and diversity

Data-based questions: Convergence and divergence of sequences

Aer a clade splits, there can be divergence of the base The hypothesis that there is ancestral convergence in

and amino acid sequences of the separated clades. The sequences was tested using two plant clades (monocots

s
more time has passed since the split, the more dierences and eudicots). There is strong evidence for monocots and

we expect due to this evolution. It therefore follows that eudicots having a common ancestor. Amino acid sequences

s
if we look back at the ancestry of two related clades, the of 51 proteins in 24 species of monocot and 44 species of

closer we get to a common ancestor, the fewer sequence eudicot were compared. Sequence convergence in the

e
dierences there will be. Figure 5 shows a theoretical ancestors of the two clades was found: the probability of

r
cladogram, with a common ancestor (P) that split to the observed pattern of sequence dierences being due to

−132

produce two ancestral clades (Q and R), which then split anything other than evolution was calculated as 1 × 10 .

y
repeatedly to form multiple clades. This is an innitesimally small chance.

1. Explain how the most probable base sequences of

a

l
ancestor P and ancestor Q c an be determined. [2]

n
2. Discuss whether more base sequence dierences are

expected between clade e and cladev or between

O
c
ancestorP and ancestorQ. [3]

i
d

3. Explain the reasons for using data from multiple

s
Q

species and multiple proteins. [2]

r
P

y
v
80

4. There are 10 protons in the universe. What is the

e
R
chance of picking the same proton at random twice
w

p
in a row? [2]

x
v

5. This research is free to access online (https://

y

o
journals.plos.org/plosone/article?id=10.1371/
i

z journal.pone.0069924). It is c alled “Beyond

n

Reasonable Doubt: Evolution from DNA

▴ Figure 5

Sequences”. Discuss whether this is a

U

suitable name. [3]

n
o
d

A4.1.3 Evidence for evolution from

i
r

selective breeding of domestic ated animals

o

and crop plants

f

Humans have bred animals selectively over thousands of years for a range of
u
x

purposes, including:

• meat and milk production; for example, sheep

l
O

• transport; for example, horses

• pets; for example, c ats.

v

If modern breeds of livestock are compared with the wild species that they most
E

resemble, the dierences are oen huge. Consider modern egg-laying hens

and the junglefowl of Southern Asia from which they have been developed; or

consider Belgian Blue c attle and the aurochs (now extinct) of Western Asia. There

is also much variation between dierent breeds of domestic ated livestock, as

shown by the diversity of dog breeds.

140
 Ecosystems

s
s
e
r
P

y
▴ Figure 6 M any breeds of dog have been developed by articial selection, starting with

grey wolves—perhaps as long ago as 30 to 40 thousand years

l
y

n
Similar patterns are observed among crop plants. Humans have selectively bred a

range of plant species for various purposes, including:

O
• food for humans; for example, wheat

i
• bres; for example, cotton

s
• cut owers; for example, roses.

y
e
As with livestock, crop plants resemble wild species of plant but are markedly

p
dierent. In addition, there are many dierent varieties of some crop plant
v

species. It is obvious that domestic ated animals and crop plants have not always

o
existed in their current forms. The only credible explanation is that changes have
i

been achieved simply by repeatedly selecting and breeding the individuals most
n

suited to human uses. This process is c alled articial selection.

The considerable changes that have occurred in domestic ated animals and
U

crop plants over relatively short periods of time show that articial selection c an
n

c ause rapid evolution. If articial selection achieved this over the 12,000 or so

years during which humans have grown crops and reared livestock, it seems
o

reasonable to assume that natural selection could have c aused major evolutionary
d

changes over the billions of years of life on E arth.

i
r

18
o

16

14
f

12
x
% CH T

10
l
O

Source: University of Mississippi /

8
a

National Institute on Drug Abuse

6
v

2
E

1995 2000 2005 2010 2015 2020

year

▴ Figure 7 Herbal c annabis is the dried owers and fruits of the plant Cannabis sativa. It

contains tetrahydroc annabinolic acid, which is converted to tetrahydroc annabinol (THC)

by heat. Through articial selection, the average THC content of c annabis sold to users has

quadrupled in 23years, increasing the risk of early-onset psychosis and schizophrenia

141
 Unity and diversity

A4.1.4 Evidence for evolution from

homologous structures

D arwin found it curious that the forelimbs of a human, mole, horse, porpoise and

bat were apparently so dierent, yet inside them are the same bones in the same

s
relative positions. D arwin c alled such similarities “unity of type”. These limbs

s
are pentadactyl, which means they have ve digits (toes or ngers). Pentadactyl

limbs are an excellent example of homologous structures—features with similar

e
anatomic al position and structure despite dierences in function.

r
Pentadactyl limbs

The pentadactyl limb consists of these structures:

y
l
Bone structure Forelimb Hindlimb

n
single bone in the humerus femur

proximal part

O
two bones in the radius and ulna tibia and bula

i
distal part

s
group of wrist or c arpals tarsals

r
ankle bones

y
series of bones in each metac arpals and metatarsals and
e

p
of ve digits phalanges phalanges
v

▴ Table 1

o
i
n

C
U

n
o
d

i
r

t
o

a
f

u
x

▴ Figure 8
l

All amphibians, reptiles, birds and mammals have the same pattern of bones (or
O

a modic ation of it), whatever the function of their limbs. The photos in Figure 8

show the skeletons of one example from each of the vertebrate classes that have
v

limbs: amphibians, reptiles, birds and mammals. All have pentadactyl limbs.
E

• Crocodiles walk or crawl on land and use their webbed hind limbs for

swimming.

• Penguins use their hind limbs for walking and their forelimbs as ippers for

swimming.

• Echidnas use all four limbs for walking and also use their forelimbs for digging.

• Frogs use all four limbs for walking and their hindlimbs for jumping.

142
 Ecosystems

You c an see dierences in the relative lengths and thicknesses of the bones.

Activity
Some metac arpals and phalanges have been lost during the evolution of the

penguin forelimb.

The explanation for homologous structures such as pentadactyl limbs is that

s
they were inherited from a common ancestor but have evolved in diverse ways

as they have become adapted for dierent functions. The common ancestor

s
of all tetrapods (four-legged vertebrates) had pentadactyl limbs, which it

probably used for walking on land. All of its descendants retain the same basic

e
arrangement of limb bones—this is D arwin’s “unity of type”.

r
There are many examples of homologous structures. They do not prove that

P
organisms have evolved into their present forms or that groups of organisms

y
mole
had common ancestry. Nor do they reveal anything about the mechanism of

evolution. However, they are dicult to explain without evolution.

l
y

n
The structures that D arwin c alled “rudimentary organs” are particularly

interesting. These are reduced structures that serve no function, now known as

O
vestigial organs. Examples are the beginnings of teeth found in embryo baleen

i
whales, despite adults being toothless; the small pelvis and thigh bones found

s
horse
in the body wall of whales and some snakes; and the appendix in humans. These

structures are easily explained by evolution: they no longer have a function so are

y
being gradually lost.
e

p
porpoise
v

A4.1.5 Convergent evolution as the origin

o
i

of analogous structures
n

There are similarities between the tails of shes and the tail ns of whales.

However, when we study these structures, we nd that they are very dierent.
U

The wings of birds and insects are also similar in some respects but close
n

examination reveals that the similarities are supercial. Such features are known

as analogous structures.
o
d

The evolutionary explanation of analogous structures is that they had dierent

origins but bec ame similar bec ause they perform the same or a similar function.
i
r

This is c alled convergent evolution.

t

bat

human
o

It c an be dicult to determine whether similar structures in dierent organisms

a

▴ Figure 9 Pentadactyl limbs

are homologous or analogous.

(not to sc ale)
f

u
x

Cladistics is increasingly used to deduce the evolutionary origins of organisms

Choose a dierent colour for e ach

and their structures. Consider the central nervous systems (CNS) of annelids,
type of bone in a pentadacty l
l

arthropods and vertebrates as an example.

O

limb, then copy and colour the

a

diagrams in Figure 9 to identify

the bones. How is e ach limb

v

use d? What fe atures of the bones

in e ach limb make it well adapte d

E

to its use?

143
 Unity and diversity

Are central nervous systems homologous or analogous?

There is a clade of animals with bilateral symmetry. Their evolved independently in these three phyla so they are

bodies have le and right sides, anterior and posterior an example of convergent evolution. They are analogous

s
ends and a need for communic ation between anterior rather than homologous structures.

and posterior. Annelids, arthropods and vertebrates

Annelids

s
achieve this communic ation via a single nerve cord

Nemerteans

running along the midline of the organism, with an

e
Brachiopods

enlarged section at the anterior end. In vertebrates, there

Platyhelminths

r
is a spinal cord and brain.

Rotifers

The development of nerve cords in annelids, arthropods

P
Nematodes

y
and vertebrates is associated with a similar pattern of

Arthropods

expression of a suite of genes c alled homeobox genes.

Vertebrates

l
This suggests that the nerve cords are homologous.

y
Hemichordates

n
However, nervous system development in other groups

Xenacoelomorphs

of bilaterians is markedly dierent. This suggests that

t
▴

O
the common ancestors of annelids, arthropods and Figure 10 In annelids, arthropods and vertebrates

i
development of a central nervous system is associated with a
vertebrates did not have the characteristic pattern of

s
similar pattern of homeobox gene expression but this has not
homeobox gene expression. The nerve cords must have

been found in other bilaterian groups

y
e

p
v

o
retina
i

nerve fibres
n

lens
U

blind spot
n

optic nerve
o
d

i
r

▴ Figure 11 The human eye (le) and the octopus eye (right) are strikingly similar in some
t

respects. However, the human eye has nerve bres in front of the retina and there is a blind
o

spot whereas in the octopus the nerve bres are behind the retina and there is no blind spot.
a

These two types of eye are the product of convergent evolution so are analogous structures
f

u
x

A4.1.6 Speciation by splitting of

l
O

pre-existing species
a

If two populations of a species become separated so they c annot interbreed and

v

natural selection then acts dierently on the two populations, they will evolve in

dierent ways. The characteristics of the two populations will gradually diverge.
E

Aer a time, they will be recognizably dierent. If the populations subsequently

merged and had the chance of interbreeding, but did not actually interbreed,

it would be clear that they had evolved into separate species. This process is

c alled speciation.

144
 Ecosystems

s
s
e
r
P

y
l
y
▴ Figure 13 In some groups, speciation has happened many times, leading

n
to large numbers of species spread over a wide area. This is known as

t
explosive species diversic ation. This has occurred in Zosterops, a genus of

▴ Figure 12 This fractal tree shows a sequence of

O
birds c alled white-eyes. There are now over 100 species in this genus, from

i
splits. In what ways does it resemble speciation? How

Afric a though Asia to Australia and New Zealand. This is the Abyssinian white-

does the evolution of species dier from the pattern in

s
eye, Zosterops abyssinica

the fractal?

y
e

p
A4.1.7 Roles of reproductive isolation and
v

dierential selection in speciation

o
i

Speciation is the formation of a new species by the splitting of an existing

species. Two processes are required for this to happen: reproductive isolation of
n

populations and dierential selection.

U

Before two populations c an split into separate species, they must stop
n

interbreeding with each other. Interbreeding c auses a mixing of genes and

therefore a blending of traits, whereas speciation depends on separation and

divergence. Biologists refer to the genes of a population as a gene pool. For

o
d

speciation to occur, there must be barriers preventing gene ow between the

gene pools of the two populations. This c an be achieved by any method of

▴
i

Figure 14 The bonobo (shown foraging

r

reproductive isolation. for insects in the river) and the chimpanzee

t
o

are both primates from the genus Pan.

a

Geographical separation is the most obvious and probably the most common cause
Bonobos are smaller and have markedly

of reproductive isolation. There may be gaps in the range of a species, which divide
dierent behaviours from chimps. The
f

it into separate populations. These gaps could be due to physical barriers that are
range of the bonobo and the chimpanzee
x

dicult to cross—for example, a mountain range, a wide river or a stretch of ocean do not overlap as they are geographic ally

between two islands. Such barriers prevent interbreeding between populations, so separated by the Congo River which
l
O

is renowned for being deep. Neither

the gene pools are separated. Geographical separation is usually associated with
a

species is thought to be able to swim.

dierences in selection pressures, which are also required for speciation.

It is thought that at one point in history

v

Natural selection c an c ause the traits of a population to change. However, the water level fell drastic ally for a time

allowing chimpanzees to cross temporarily.

if it operates in the same way in two populations of a species, their traits will
E

It is thought that these migrants bec ame

remain the same and they will not become separate species. Where there are

geographic ally isolated from their ancestors

signic ant dierences in selection, this is c alled dierential or divergent selection.

when the water level of the Congo rose

Dierential selection c auses the traits of the populations to become more and

again. This founder population, being

more dierent; when this divergence is judged by taxonomists to be signic ant,

subject to dierent selection pressures,

the populations are classied as separate species.

diverged from chimpanzees to become

bonobos

145
 Unity and diversity

To understand how there c an be dierential selection, consider a new population

of a species that has been established by migration to an island. Any or all of

these factors might be dierent from the other parts of the species range:

• climate—temperatures, rainfall and other aspects

s
• predation—there might be dierent predators or even no predators in

some are as

s
• competition—there might be more or less competition for resources.

e
The lava lizards of the G alápagos archipelago are an example of geographic al

r
isolation and speciation.

y
l
Speciation in lava lizards

n
Speciation oen occurs aer a population of a species islands, there are six closely related but dierent species,

O
extends its range by migrating to an island. This explains formed by migration to an island, reproductive isolation

i
the large numbers of endemic species on islands. An and divergence due to dierential selection.

s
endemic species is one that is found only in a certain
Cladistics research suggests that there were two separate

geographic al area.
migrations of lava lizards from mainland South Americ a to

y
The lava lizards of the G alápagos Islands are an example. the Galápagos. One of these migrations populated S an
e
One species (Microlophus albemarlensis) is present on all Cristóbal and M archena; the other populated all the other

p
the larger islands of the archipelago. On six smaller islands apart from Genovesa.
v

o
i

Pinta
n

 

Genovesa

Marchena
U

Santiago
o
d

Santa Cruz
Fernandina San Cristóbal
i
r

Santa Fe
t
o

▴ Figure 16 Galápagos lava lizard Microlophus

Isabela
a

albemarlensis on S anta Cruz Island

Española
f

Santa Maria
u
x

key
l
O

M. bivittatus None
v

▴ Figure 15 Distribution of lava lizards in the Galápagos Islands

E

146
 Ecosystems

Data-based questions: Flightless steamer ducks

Steamer ducks are members of the genus Tachyeres and Analysis of mitochondrial DNA base sequences suggests

inhabit southern Chile and Argentina. Recent research that the species on the M alvinas diverged from the three

s
suggests that there are four species. Two of them are continental species between 2.2 and 0.6 million years

ightless and live on the coast of Chile and Argentina. A ago and that the continental species diverged from a

s
third species c an y and occurs both on the coast and common ancestor about 15,000 years ago.

inland, with its range overlapping those of the ightless

e
There have been repeated glaciations with extensive

species. The fourth species of steamer duck occurs on

ice cover and low sea levels in the areas inhabited by

r
the M alvinas or F alklands islands to the east of Argentina.
these ducks. During the Great Patagonian Glaciation

This species has ightless coastal populations and also

(GPG) about a million years ago, much of southern Chile

y
populations that c an y and only breed on inland lakes.
and Argentina was ice-covered and the sea level was

The map shows the ranges of the four species.

200metres lower than it currently is. During the L ast

l
Glacial M aximum (LGM) 15,000 years ago, the ice cover

n
Fuegian flightless steamer duck ( Tachyeres pteneres)
was not as extensive and sea levels did not drop as much.

t
Chubut flightless steamer duck ( T.leucocephalus) 1. Suggest how populations of steamer duck could

O
have become reproductively isolated, allowing

i
Malvinas/Falklands flightless steamer duck

T. brachypterus to diverge from the continental

(T. brachypterus)

s
species. [2]

fling steamer duck (T. patachonicus)

r
2. Discuss, with reasons, whether there is currently

y
interbreeding between T. pteneres and
Chile
e
Argentina

p
T.leucocephalus [2]

–200 metres
v

sea level 3. Suggest how T.pteneres and T.leucocephalus

o
could have evolved from a common ancestor
i

15,000 years ago. [2]

n

4. Discuss whether T.patachonicus is likely to cross-

breed with T.pteneres and T.leucocephalus. [2]

U

5. Predict whether T.brachypterus is likely to diverge

n

into ightless and ying species. [2]

o
d

i
r

t
o

GPG ice limit

f

u
x

l
O

a
v

▴ Figure 18 T. brachypterus showing the rapid method of

swimming characteristic of steamer ducks, using legs and wings

E

and resembling a paddle steamer. The genus name Tachyeres

▴ Figure 17

means “fast rower ”

Source: Fulton et al, Proc. R. Soc. B (2012) 279,

2339–2346 doi:10.1098/rspb.2011.2599

147
 Unity and diversity
LHA

A4.1.8 Dierences and similarities between

sympatric and allopatric speciation

Speciation is the process by which one species splits into two or more separate

species. It c an only happen if populations of a species are reproductively

s
isolated. Geographic al separation, described earlier in this chapter, is an obvious

s
means of reproductive isolation. When populations in dierent geographic al

areas become separate species, allopatric speciation has occurred.

e
It is also possible for a population of a species living together in one geographic al

r
area to split into two populations that do not interbreed. If they remain

P
reproductively isolated, the populations could diverge to form separate species.

y
This is c alled sympatric speciation. Sympatric means “same homeland” and

allopatric means “dierent homelands”.

l
y

n
Reproductive isolation in sympatric populations may be a consequence of

behavioural dierences in animals and temporal dierences in animals or plants.

O
Sympatric speciation is certainly much less common than allopatric speciation

i
and it is dicult to be sure whether closely related species living in the same

s
geographic al area are the product of true sympatric speciation, or allopatric

speciation followed by migration. Examples of reproductive isolation due to

y
behavioural and temporal separation
e are given here.

p
v

o
Behavioural separation
i
n

Two forms of a species of cichlid sh (Astatotilapia yellower) and sensitivity of retinal pigments to dierent

calliptera) have been discovered in Lake Massoko, a wavelengths of light. Genetic dierences have been found

700metre wide crater lake in Tanzania. One form prefers to between the two forms and experiments have shown that
U

feed near the shore (littoral) and the other in deeper water females tend to select a mate who is genetically similar to
n

(benthic). The two forms have adaptations corresponding themselves. This is an example of behavioural separation,

to these preferences—body size and shape, structure of which reduces the mixing of genes between the two forms.
o
d

the jaw and teeth, coloration of breeding males (bluer or Over time, this may result in speciation.
i
r

t
o

a
f

u
x

l
O

a
v
E

▴ Figure 19 Lake M asoko with a male littoral (yellow) morph Astatotilapia calliptera, a male

benthic (blue) morph and a female mouthbrooding eggs

148
 Ecosystems

LHA
Temporal separation

The winter pine processionary moth (Thaumetopoea with each other as there is temporal separation: the two

pityocampa) lives in countries around the Mediterranean. or three days of adult life happen at dierent times of

s
Its life cycle takes one year to complete. Adults emerge in year. It seems reasonable to assume that the two forms

summer or early autumn and live for just two or three days. will diverge, bec ause dierent adaptations are needed

s
During that brief time they mate and females then lay by larvae active in summer or winter. If the divergence

100–200 fertilized eggs. The eggs hatch into larvae that becomes great enough, sympatric speciation will have

e
feed during the autumn and winter on leaves of pine and occurred.

r
cedar trees. In February or M arch, the larvae migrate in

head-to-tail processions down from the trees and to their

y
pupation sites underground in soil. The pupae develop

into the next generation of adults, emerging at the same

l
time of year as did their parents.

n
In one area of Portugal, researchers have discovered a

population of this species that has dierent timings for all

O
stages in its life cycle. Adults emerge in M ay or June and

i
larvae feed and grow through the summer, rather than the

s
winter. In the warm summer conditions, the larvae grow

quickly and are ready to pupate by the end of September.

y
The more common form of the moth, with winter larvae,
e
also lives in this area of Portugal—they are sympatric.

p
The timing of the life cycle is a heritable trait so must
v

be determined genetic ally. The two forms never mate ▴ Figure 20 Winter processionary moth larvae in a procession

o
i
n

A4.1.9 Adaptive radiation as a source

U

of biodiversity
n

Characteristics that make an individual suited to its environment or way of life are

called adaptations. This term is used because the t between structure and function
o
d

is developed over time, by a process of modication. The process of modication is

“adaptation” and a trait developed by this process is “an adaptation”.

i
r

Species extend their range if a group of individuals migrates to a new area. These
o

individuals are the founders of a new population. If they cannot interbreed with
a

other populations, the traits of the new population will tend to diverge from the rest
f

of the species. This is partly due to chance, oen aided by the small initial number
x

of founders. It is also partly a result of adaptation to dierences in the environment.

Another factor that can cause rapid adaptation in a new population is the availability
l
O

of an ecological niche that is not being fully exploited by other species.

a

Speciation and adaptation to new niches have happened repeatedly in some

v

groups. This is c alled adaptive radiation; the word “radiation” means spreading

out. In this c ase, the radiation is ecologic al, rather than geographic. Adaptive
E

radiation is dened as a pattern of diversic ation in which species that have

evolved from a common ancestor occupy a range of ecologic al roles. It is a

source of considerable biodiversity. Bec ause of the diversity of ecologic al niches,

adaptive radiation minimizes competition between species so they c an coexist.

Even if the process of speciation is allopatric, migration c an occur and closely

related species c an then live sympatric ally.

149
 Unity and diversity
LHA

Darwin’s nches

Galápagos nches are the best known example of

adaptive radiation. O ver the past 2.3 million years,

s
14species of nch have evolved from a common ancestor

on the islands of the Galápagos archipelago. These

s
nches have become adapted to dierent food sources:

leaves, fruits, pollen, nectar, small so seeds, large hard

e
seeds, insects on leaves and insects under bark. The beaks

r
of the nches show particularly clear adaptations. Up to

10 species of Galápagos nch have been found living

y
together in one loc ality. It is unlikely that this would be

possible without adaptive radiation—there would be too

l
much competition.

n
▸ Figure 21 This statue depicts the young Charles D arwin stepping

O
onto the Galápagos islands in 1835. He studied the nches on these

i
islands and later wrote: “The most curious fact is the perfect gradation

s
in the size of the beaks in the dierent species of Geospiza, from one

as large as that of a hawnch to that of a chanch, and … even to that

y
of a warbler… Seeing this gradation and diversity of structure in one

small, intimately related group of birds, one might really fancy that
e

p
from an original paucity of birds in this archipelago, one species had

been taken and modied for dierent ends” (D arwin, 1839)

v

o
i
n

Brocchinias—adaptive radiation of bromeliads on the Guiana Shield

Brocchinia is a genus of bromeliads. The 20 species grow

U

on the Guiana Shield in southern Venezuela and Guyana.

n

The common ancestor of Brocchinia species diverged

from all other bromeliads 20 million years ago and

o
d

diversic ation within the genus has been happening for at

least the last 13 million years.

i
r

The sandstone rock of the Guiana Shield yields nutrient-

t

decient soils that c an limit plant growth. Plants which

o

develop successful nutrient-c apture strategies therefore

a

have a competitive advantage. Brocchinias have

f

developed a greater diversity of strategies than any other

x

genus of plants. For example:

l

• Brocchinia prismatica relies solely on its roots

O

growing through the soil for a supply of nutrients.

• Brocchinia reducta has curved vertic al leaves

v

that together form a tank in which water collects.

Chemic als are secreted into the uid to give it a sweet

E

nectar-like smell, which attracts insects. The wax

covering the leaves is particularly slippery, so insects

fall into the uid and c annot esc ape. The uid is very

acidic and contains digestive enzymes, so trapped

insects are killed. Specialized hairs on the leaves

▴ Figure 22 Brocchinia reducta, Mount Roraima,

absorb mineral nutrients released by digestion.

Venezuela

150
 Ecosystems

LHA
• Brocchinia acuminata has expanded leaf bases

creating chambers in which ant colonies live. Dead

ants and detritus from ant activities are digested in

uids at the base of these chambers. Roots grow

s
into the uid and absorb the nutrients released by

digestion.

s
• Brocchinia micrantha grows very large and collects

e
litres of rainwater at the base of each of its leaves.

Dead leaves and other plant detritus falling into

r
these water tanks are digested, providing a supply of

nutrients to the plant.

y
• Brocchinia tatei also has leaf bases that collect water

l
and falling plant debris. It c an live on the ground or as
▴ Figure 23 Brocchinia micrantha, K aieteur National Park,

n
an epiphyte growing on the trunks and branches of
Guyana

trees. Nitrogen-xing cyanobacteria grow in its tanks

t
and supply the plant with nitrogen compounds.

O
i
s
r

y
A4.1.10 Barriers to hybridization and sterility
e

p
of interspecic hybrids as means of preventing
v

the mixing of alleles between species

o
i

I n t e rs p e c i f i c hy br i d s a re pro du c e d by c ro ss - b re e d i n g me mb e rs of di ffe re n t
n

s pe c i e s . Th e hy br i d s c o mb i n e tra i ts of th e species th a t w e re c ro ss e d .

Hy br i d i z a ti o n is o f te n do n e d e l i be ra t e l y by pl a n t or animal b re e d e rs . Th e
U

mu l e was pro b a b l y the f i rs t hy br i d, p ro du c e d by c ro ss - b re e d i n g a h o rs e with

a d o n ke y ( Eq u us c a b a l lus × Eq u us as in us ). Mules c o mb i n e useful t ra i ts of

n

th o s e two s pe c i e s and also h ave what is k n ow n as hy b r i d vi go u r. They h ave

th e re fo re been de l i be ra t e l y b re d fo r 5 ,0 0 0 ye a rs or m o re. Ho rs e s h ave 64

o
d

c h ro m o s o m e s and d o n ke ys h ave 62 so a mule has 63 . This c auses p ro bl e m s

in me i o s i s . Fo r th a t re a s o n and other ge n e t i c i n c o m pa ti bi l i ti e s , mules a re

i
r

ne arly a l w ays s te r i l e.
t
o

Plant breeders oen use interspecic hybridization to produce new varieties. The rst
a

person known to have done this was Thomas Fairchild who, in the early 18th century,
f

crossed carnations with Sweet Williams (Dianthus caryophyllus × Dianthus barbatus).

u
x

The hybrids showed traits of both parents and were nicknamed “Fairchild’s Mule”.

Both parent species have 30chromosomes, but even so Fairchild’s Mule was sterile.
l
O

This is very common in interspecic hybrids produced by breeders.

a

Interspecic hybridization sometimes happens naturally if the ranges of

v

closely related species overlap in an ecosystem. Like articial hybrids, natural

interspecic hybrids are oen totally or partially sterile so they c ause little or no
E

permanent mixing of alleles between the parent species.

In evolutionary terms, the resources that a parent expends on producing a sterile

hybrid are wasted. It is not surprising, therefore, that many species have evolved

barriers to prevent the development of hybrid ospring. A hybrid zygote may be

produced but it is likely to die during development.

151
 Unity and diversity
LHA

Eve n few e r re s o u rc e s a re wasted if no mating ta k e s place between d i f fe re n t

s pe c i e s . In a n i ma l s , th i s is one of th e fu n c ti o n s of c o u r ts h i p be h av i o u r : an

individual c an che ck w h e th e r a po te n t i a l pa r t n e r is a m e mb e r of its ow n

s pe c i e s by l o o ki n g fo r d i s ti n c ti ve be h av i o u ra l fe a t u re s . Th e re a re o ft e n s e ve ra l

s ta ge s in c o u r t s h i p, with re j e c ti o n at a ny s ta ge if th e c h a ra c t e r i s ti c b e h av i o u r

s
pa tte r n of th e s pe c i e s is not di s p l aye d . To p re ve n t i n te rs p e c i f i c hy b r i d i z a t i o n ,

courtship b e h avi o u r needs to be di s t i n c t i ve. Th i s ex pl a i n s th e i m me n s e

s
di ve rs i t y, p a r ti c u l a r l y among bi rds — b i rds of pa ra di s e in P a pu a New Guine a,

e
fo r exa mp l e.

r
In some c ases, closely related species do have ranges that overlap and

these species produce fertile interspecic hybrids. This c an happen where

y
geographic al separation has allowed speciation but migration brings the newly

separated species back together again. If barriers to hybridization have not

l
developed, there may be mixing of alleles and speciation may be reversed. This

n
c an also happen if humans bring species together that would naturally have

remained geographic ally separated. For example, on some Hawaiian islands the

t
native duck (Anas wyvilliana) is hybridizing with introduced non-native mallard

O
i
(Anas platyrhynchos), forming hybrid swarms with a mixture of traits from both

s
species. As a result, Anas wyvilliana faces extinction through hybridization, with a

consequent loss of biodiversity.

y
e

p
Courtship in Clark’s grebes
v

Clark’s grebe (Aechmophorus clarkii) of western North Americ a has an

elaborate courtship display that c an be

o
viewed in video clips on the internet.
i

However, the closely related Western grebe (Aechmophorus occidentalis)

n

has the same display and these species do sometimes mate and produce

hybrid ospring. Two possible hypotheses explain this apparent anomaly:

U

either these two species have not had enough time since diverging to evolve
n

dierences in their courtship displays, or they should not be regarded as

separate species.
o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

▴ Figure 24 Courtship in Clark’s grebes involves a

sequence of distinctive and coordinated actions, which

establish and reinforce the bond between male and female

152
 Ecosystems

LHA
H

s
O O

s
e
H

r
P
O H

y
l
y

n
t
▴ Figure 25 In honey be es (Apis mellifera) fertile females (que ens) only ever mate with fertile males (drones) on one mating ight.

O
i
When que ens are re ady to mate, they y in the e arly aernoon to spe cial drone congre gation are as, which are 10–20 m above the

ground and about 100 m in diameter. D rones f rom dierent colonies have alre ady assemble d there. Both que ens and drones typic ally

s
y 2–3 km f rom their colony to re ach a drone congre gation are a. Q ue ens rele ase the pheromone (e)-9-oxo-2-de cenoic acid (le) as a

r
sex attractant for drones, which have re ceptors for this pheromone on their large antennae (right). Crowds of drones chasing que ens

y
resemble comets shooting ac ross the sky. D uring the mating ight, que ens copulate with up to 20drones. This provides all the sperm
e
ne e de d to fertilize hundre ds of thousands of e ggs that a successful que en will lay over several ye ars. How is interspe cic hy bridization

p
prevente d in honey be es?
v

o
i

A4.1.11 Abrupt speciation in plants by

n

hybridization and polyploidy

U

A polyploid organism has more than two sets of homologous chromosomes.

n

Polyploidy is a consequence of the duplic ation of chromosomes in a cell

without a subsequent cell division, so it is whole-genome duplic ation. Genome

o

sequencing studies show that it has happened many times in evolution.

d

If whole genome duplic ation happens in a diploid cell, the result is four sets
i
r

of homologous chromosomes, so the cell is tetraploid. Bec ause all the sets of
t

chromosomes come from the same organism, it is c alled an autotetraploid.

o

Autotetraploidy is usually associated with low fertility, bec ause there are four

homologous chromosomes of each type and mis-pairing is very likely during

f

meiosis. O ver time, there c an be genetic changes that overcome this problem,
x

allowing autotetraploid populations to become established.

l
O

S and rock-cress (Arabidopsis arenosa) is an example of the establishment of

a

autotetraploid populations. Diploid plants of this species (with 16 chromosomes)

only grow in eastern and southeastern Europe. Part of this area, in the
v

Balkan Peninsula and Western C arpathian mountains, has both diploids and

autotetraploids. It is thought that the autotetraploids originated here before

E

spreading to western Europe and Sc andinavia, where only autotetraploid plants

have been found.

Meiosis in an autotetraploid individual produces diploid cells and therefore

diploid gametes. If these fuse with haploid gametes from an individual that

is diploid, triploid ospring are produced (see Figure 26). These may grow

vigorously but they are very unlikely to perform meiosis successfully, so are sterile.

153
 Unity and diversity
LHA

According to the biologic al species denition, diploids and autotetraploids

should be regarded as separate species. However, autotetraploids are usually

very similar in morphology to diploids, so taxonomists may be reluctant to

recognize them as new species. They are also relatively uncommon in nature,

perhaps bec ause the similarities with the original diploid population make

s
competition likely.

s
e
diploid
AA

r
polyploidy

y
autotetraploid AAAA

l
meiosis

n
gametes may

be produced

O
haploid gamete

i
from a diploid

s
r

y
but interbreeding
e
with a diploid yields AAA

p
a sterile triploid
v

o
▴ Figure 26 Autotetraploidy: the symbol A represents one

diploid
i

AA BB haploid set of chromosomes

parents
n

of different

species

interspecific
U

hybridization
Another type of polyploidy is the result of a two-stage process.
n

1. Individuals from dierent species cross-breed. The resulting interspecic

sterile

AB
hybrid has two sets of chromosomes, with one set from each of the two
interspecific
o
d

dierent parent species. Unless these two species are very closely related,
hybrid

polyploidy
chromosomes will not form homologous pairs when meiosis is attempted,
i
r

so the hybrids will be sterile.

t
o

2. If any cell in the sterile interspecic hybrid duplic ates its chromosomes but
allotetraploids AABB AABB
a

does not then divide, the cell will have four sets of chromosomes. It is an
meiosis
f

allotetraploid bec ause the four sets of chromosomes are from two dierent
u

species. More of these allotetraploid cells c an be produced by mitosis. It is

x

AB AB

likely that these allotetraploid cells will be able to divide by meiosis bec ause
l

there are two homologous chromosomes of each type, which c an reliably

O

allotetraploids form pairs. By becoming an allopolyploid, the interspecic hybrid will

can interbreed to overcome its fertility problems.

v

produce more

allotetraploids Allotetraploids c an interbreed with other allotetraploids, but not with either of
E

the diploid parent species. They are therefore a new species and, as they have

a mixture of traits from both parent species, they are usually recognized and
▴ Fi g u re 27 A l l o t e t ra p l o i d y: t he

named as a distinct species. M any species have been produced by this two stage
sym b o l s A a nd B re p re s e n t d i f fe re nt

process, especially in the plant kingdom—for example, in the genus Persicaria

ha p l o i d sets of c hro m o so m e s

154
 Ecosystems

LHA
Horse chestnut trees

Horse chestnut trees (Aesculus hippocastanum) are native

to northern Greece. Red buckeye trees (Aesculus pavia)

s
are native to the southern United States. Both species

were introduced to Germany, where they hybridized.

s
The initial hybrid combined traits from both parents but

was sterile. A shoot on the tree then developed that was

e
fertile and produced seeds. These seeds germinated

r
to produce more trees with the same traits as the

original hybrid. What is the likely explanation for these

y
observations? The hybrid trees are regarded as a new

species, c alled Aesculus × carnea. Figure 28 shows a

l
specimen in the author ’s garden.

n
◂ Figure 28

O
i
s
Hybridization and polyploidy in the genus Persicaria

y
There are over 100 species in the genus Persicaria, with

species occurring in most parts of the world. There is

e

p
evidence for at least 15 species in the genus having
v

originated by allopolyploidy. One of these is Persicaria

o
maculosa (2n = 44 chromosomes), which is native to
i

Europe and Asia. (It is an introduced alien in other parts

n

of the world.) Research indic ates that this species arose

by hybridization between Persicaria foliosa (2n = 22) and

Persicaria lapathifolia (2n = 22), followed by a doubling

U

of the chromosome number.

n

▴ Figure 29 Persicaria maculosa

o
d

i
r

Linking questions
t
o

1. How does the theory of evolution by natural selection predict and explain the unity and diversity of life on E arth?
a

a. With reference to an example, outline the concept of adaptive radiation. (A4.1.9)

f

b. Outline the features shared by all cells. (A2.2.4)

x

c. Discuss the relationship between niche and convergent evolution. (B4.1.7)

l
O

2. What counts as strong evidence in biology?

a. Explain how the emergence of antibiotic resistance is predicted and explained by the theory of evolution by
v

natural selection. (A4.1.1)

E

b. Discuss the experimental evidence that conrmed that DNA is the genetic material. (A1.2.14)

c. O th e r than th e e m e rg e n c e of a n ti bi o t i c re s i s t a n c e, outline the e vi de n c e that s u pp o r ts the the ory of

e vo l u ti o n by n a tu ra l s e l e c ti o n . (A 4 .1 )

155
 A4.2 Conservation of biodiversity

s
What factors are c ausing the sixth mass extinction of species?

s
A number of factors threaten biodiversity, including the loss

e
of habitat, exposure to pollution, overexploitation, threats

from invasive species and climate change. The image

r
shows a Red fox (Vulpes vulpes) consuming an Arctic fox

(Alopex lagopus) it has killed. The Arctic fox faces a number

y
of threats. What habitat changes is it facing due to climate

change? How is climate change impacting the distribution

l
of its prey, its predators and competitor species that

n
occupy the same niche? Is the range of temperate species

having an impact on the Arctic fox?

O
▴ Figure 1 Red fox (Vulpes vulpes) consuming an

i
Arctic fox (Alopex lagopus) it has killed, Wapusk

s
National Park, C ape Churchill, M anitoba, C anada

y
e
How c an conservationists minimize the loss of biodiversity?

p
v

One approach to minimize the loss of biodiversity is to

o
counteract the main factors that threaten extinction. How
i

c an conservationists respond to threats to biodiversity due

n

to climate change, habitat loss and the spread of invasive

species? What are examples of in situ and ex situ conservation

U

measures? What challenges have to be surmounted by both?

The image shows Young white storks (Ciconia ciconia) being

n

fed sh. These birds are being raised for reintroduction to the

wild. What type of conservation approach is this?

o
d

i
r

▸ Figure 2 Young white storks (Ciconia

t

ciconia) being fed sh

o

a
f

SL and HL
u
x

A4.2.1 Biodiversity as the variety of life in all its forms, levels and combinations

A4.2.2 Comparisons between current number of species on E arth and past

l
O

levels of biodiversity
a

A4.2.3 C auses of anthropogenic species extinction

A4.2.4 C auses of ecosystem loss

v

A4.2.5 Evidence for a biodiversity crisis

A4.2.6 C auses of the current biodiversity crisis

E

A4.2.7 Need for several approaches to conservation of biodiversity

A4.2.8 Selection of evolutionarily distinct and globally endangered species for

conservation prioritization in the EDGE of Existence programme

156
 Ecosystems

A4.2.1 Biodiversity as the variety of life in all

its forms, levels and combinations

The word biodiversity is an abbreviation for “biologic al diversity”. Diversity

has been dened as “variety or multiformity, a condition of being dierent in

s
character and quality”. It is the opposite of unity. Biology is the study of life,

s
so biodiversity is the variety or multiformity of life. It exists at multiple levels,

including:

e
• Ecosystem diversity—variety in the combinations of species living together in

r
communities. This diversity is partly due to the very varied environments on

E arth. It is also due to the geographic al ranges of organisms.

y
• Species diversity—the many dierent species on the evolutionary tree of life.

These species have varied body plans, internal structure, life cycles, modes

l
of nutrition and more.

n
• Genetic diversity within species—variety in the gene pool of each species.

t
There is variation both between geographic ally separated populations and

O
i
within populations. Species with only a few surviving individuals inevitably

s
have little genetic diversity and problems due to inbreeding.

y
e

p
v

o
i
n

◂ Figure 3 Living land-based vertebrate

U

species are not distributed evenly around

n

the planet. The highest concentration of

diversity is shown in red, in regions around

the equator. Diversity decreases closer to

o
d

the E arth’s poles; this is shown by (in order)

orange, yellow, green and blue shading

i
r

t
o

A4.2.2 Comparisons between current

f

number of species on E arth and past levels

x

of biodiversity
l
O

Fewer than two million species have been named and described. M any more

remain undiscovered, so it is impossible to state with condence the current

v

number of eukaryotic species on E arth. Estimates vary widely but are mostly

between 2 and 10 million. With prokaryotes, there are too many uncertainties
E

for reliable estimates of numbers of species to be made.

It is even more dicult to estimate how many eukaryotic species lived on E arth in

the past. Relative levels of biodiversity c an be deduced from fossil evidence. This

shows large variations. In particular, there have been ve mass extinctions when

many species disappeared. The most recent mass extinction was 66 million years

ago, at the end of the Cretaceous period. This occurred when a huge asteroid

157
 Unity and diversity

collided with the E arth. The consequent environmental disruption c aused many
areneg fo

species to die out, including all non-avian dinosaurs. The previous four mass

extinctions have been attributed to volc anic activity and major changes to the

80,000

atmosphere and global climate.

rebmun

s
Between mass extinction events, biodiversity tends to rise gradually, with new

forms of life evolving. For example, the extinction of the non-avian dinosaurs and

s
20,000

other groups at the end of the Cretaceous was followed by evolution of many

e
new species of birds and mammals.

1750 1950

There have been no mass extinction events for 66 million years now. As a result,

r
year

biodiversity has been able to undergo a sustained increase: it is probably higher

P
now than it has ever been. However, human activity is causing what is predicted to

y
be the sixth mass extinction, so this peak of biodiversity is unlikely to be sustained.
seilimaf fo

5,000

l
slamina

n
5,000
rebmun

t
eniram fo

O
4,000

i
1,000

s
3,000
areneg fo srebmun

y
1750 1950

year 2,000
e

p
▴ Figure 4 One approach for predicting
v

1,000

the number of species, genera, families

o
and higher taxa is to extrapolate from past
i

discovery rates. The graphs show numbers 0

n

542 500 450 400 350 300 250 200 150 100 50 0
of genera and families in the animal

kingdom. The lines showing an asymptote millions of years ago

represent the expected total numbers

U

▴ Figure 5 This graph shows the numbers of marine animal genera known from fossil

Source: Mora C, Tittensor DP, Adl S, Simpson

n

evidence over the 542 million years since the start of the C ambrian period. It shows that

AGB, Worm B (2011) How M any Species

biodiversity of animals in marine habitats is probably higher now than it has ever been. Other

Are There on E arth and in the Ocean?.

groups of organisms are likely to have followed the same trend. During the C ambrian period,
PLOS Biology 9(8): e1001127. https://doi.
o
d

there was a major diversic ation of animals and other multicellular organisms, known as the
org/10.1371/journal.pbio.1001127

C ambrian explosion
i
r

t
o

Patterns, trends and classic ation

f

Ornithologists are scientists who study birds. The graph

x

in Figure 8 shows the incidence of “corrections” in the

classic ation of North Americ an bird species since the

l
O

formation of the Americ an Ornithologists Union in 1883.

a

For example, Traill’s yc atcher was split into two distinct

species in 1973: alder and willow yc atchers. O ver

v

much of the 20th century, the trend was to reduce the

E

number of species, by uniting those that showed strong

similarities (“lumping”). Since the 1980s, that trend has

changed towards more splitting due to recognition of

▴ Figure 6 Alder ▴ Figure 7 Willow

the phylogenetic distinctiveness of populations that were

yc atcher yc atcher

previously considered a single species.

158
 Ecosystems

1. Suggest why the 1935 public ation of a paper 3. The graph is cumulative and shows some periods

proposing the biologic al species concept might when there was relatively little “lumping” or

have led to the tendency towards “lumping”. “splitting”. What were these periods and what could

the reasons have been?

2. Suggest why the improvement in DNA technology in

s
the 1980s might have led to an increasing tendency

towards splitting.

s
stilps

e
140
ro spmul fo

r
P

y
100

Source: Montgomerie, B. (2019)

rebmun

Lumpers and Splitters, Americ an

l
lumps
Ornithologic al Society.

n
50
evitalumuc

O
i
splits

s
0

1880 1900 1920 1940 1960 1980 2000 2020

y
▴ Figure 8 Cumulative graph showing the total number of “lumps” or “splits”
e
in bird species in North Americ a

p
v

A4.2.3 C auses of anthropogenic species

o
i
n

extinction

Species extinction is a natural process. If it is balanced by evolution of new

U

species, biodiversity does not decrease. Extinctions have been happening for
n

billions of years, but current rates are very high. Five main types of c ause c an be

identied and all of them are anthropogenic (due to human activities).

o
d

1. O verharvesting

Humans take plants and animals from natural ecosystems by hunting animals,
i

harvesting plants for food or medicines, logging forests to obtain timber, and
r

shing in freshwater or marine ecosystems. If this happens at a faster rate than

o

a species c an reproduce, extinction will occur. For example, current shing

a

rates are certainly unsustainable. Sometimes only part of an animal is used,

f

for example, shark ns, elephant tusks and tiger bones.

u
x

2. Habitat destruction
l

Agriculture began about 12,000 years ago in the Middle E ast. Today, over
O

13billion hectares of land are cultivated or used for rearing livestock. Natural
a

habitats such as forests or grasslands were destroyed so that land could be

v

used for agriculture. This led to the loss of some species. About 6,000 years

ago, humans began to establish towns and cities, c ausing more losses of
E

natural habitat.

3. Invasive species

When alien species are introduced to ecosystems, they c an drive native

species to extinction by predation, spreading of pests and diseases, or

competition for resources. Endemic species c an also become extinct if

159
 Unity and diversity

they hybridize with aliens. Some introductions have been deliberate—for

example, possums and domestic c ats in New Zealand. In other c ases, they

are accidental and a consequence of transport on boats and airplanes.

4. Pollution

Chemic al industries produce a vast range of substances that are used and

s
then disc arded or released into the environment. No part of the world is

s
unaected by pollution—for example, lead from the Roman era c an be

detected deep in Arctic ice, and plastic waste washes up on beaches in the

e
most remote parts of the world. Burning of fossil fuels, agriculture, mining, oil

extraction and pharmaceutic als are all major sources of pollutants.

r
5. Global climate change

y
Plants and animals adapt to the conditions that they experience. If conditions

change gradually, they will evolve to survive. However, human activities are

l
c ausing very rapid changes in temperature, rainfall, snow cover and other

n
environmental variables on E arth. Some species will be able to adapt or

migrate, but others face extinction. For example, coral species may not adapt

O
quickly enough to survive in rising sea temperatures.

i
There are many well-understood c ases of species extinction. Three examples are

s
described here.

y
e

p
Giant moas (Dinornis novaezealandiae)
v

o
The megafauna of Afric a has declined but most species
i

still survive. In other parts of the world, many of the

n

largest animals have become extinct during the last

20,000 years. In at least some c ases, this happened as

U

humans spread around the world and began hunting the

loc al megafauna. In North Americ a, there is evidence

n

that humans hunted mammoths and wild horses to

extinction about 13,000 years ago. Smilodons (sabre-

o
d

toothed c ats) also disappeared at this time, probably due

to loss of their prey.

i
r

Moas were a group of ightless birds, native only to

t

New Zealand. There were nine species, the largest of

o

which were the giant moas—Dinornis novaezealandiae

on the North Island and Dinornis robustus on the South

f

Island. They grew up to 3.6 m tall and had a mass of

x

approximately 230 kg. New Zealand was not settled by

l

humans until the arrival of Polynesians in the 13th century,

O

▴ Figure 9 Painting of ▴ Figure 10 Skeleton of Dinornis

who bec ame the M āori iwi.

a

It then took less than 200

Dinornis novaezealandiae novaezealandiae in the British

years for all species of moa to be hunted to extinction.

by William Frohawk Natural History Museum

v
E

160
 Ecosystems

Atitlán grebe (Podilymbus gigas)

C ats, rats and other alien species spread by humans are In 1966, a refuge was established for Atitlán grebes

one of the major c auses of extinction. Where it is not too and numbers rose to 210 by 1973. Unfortunately an

s
late, eradic ation programmes c an be very successful. earthquake in 1976 fractured the lake bed and the water

On Henderson Island in the South Pacic, for example, level fell. This c aused a marked decline in bird numbers,

s
three bird species have already been driven to extinction with only 32 grebes surviving in 1983. Most of these were

by Pacic rats, including the Henderson imperial pigeon hybrids with the pied-billed grebe (Podilymbus podiceps).

e
(Ducula harrisoni). Four other endemic species of land Two birds were seen in 1989 but they then disappeared

r
bird are threatened. A rat-eradic ation programme, led and the Atitlán grebe was declared extinct.

by the RSPB, has reduced rat numbers. However, until all

y
the rats have been removed, Henderson Island’s endemic

birds will remain at risk of extinction.

l
For the Atitlán grebe (Podilymbus gigas) it is too late.

n
This large grebe was endemic to L ago de Atitlán in

Guatemala, at an altitude of 1,700 m. It had small wings

O
and was ightless. The decline of the Atitlán grebe began

i
in 1958, when two species of black bass (Micropterus

s
dolomieu and Micropterus salmoides) were introduced

to the lake to try to promote tourism by anglers. These

y
sh multiplied and competed for the crabs and sh that e
were foods for the grebes. The bass also predated grebe

p
chicks. Numbers of Atitlán grebe declined from 200 in
v

1960 to 80 in 1965.

o
▴ Figure 11 Atitlán grebe, now extinct
i
n

Mount Glorious torrent frog (Taudactylus diurnus)

U

Amphibians breed in water but spend most of their adult spe cies and an infe ctious chytrid fungal dise ase may

life in terrestrial habitats, so they are particularly vulnerable also have contribute d to this sudden and re grettable

to extinction due to habitat destruction. The Mount spe cies extinction.

o
d

Glorious torrent frog lived in rainforests in three mountain

ranges in northeastern Australia. When rst described in

i
r

1966, it appeared to be relatively common in mountain

t
o

streams. However, its populations declined rapidly and it

a

was probably extinct by 1980.

f

The principal c ause of extinction w as deforestation:

u

over 10,000 he ctares of tre es were cle are d from the

x

range of T. diur nus during the 20th century. This altere d

l

w ater ows and inc re ase d turbidity in the stre ams where
O

the frogs bre d. Alien feral pigs were another factor.

They pre date d the f rogs and contaminate d the w ater

v

of stre ams by churning up mud. Inv asive alien plant ▴ Figure 12 Mount Glorious torrent frog
E

A4.2.4 C auses of ecosystem loss

O ver much of the E arth’s surface, human activity has c aused the loss of natural

ecosystems. In many areas, the c auses of loss were direct—the ecosystem

was cleared to allow other forms of land use. In other areas, the c auses of loss

were indirect and unintentional. An ecosystem consists of interacting and

161
 Unity and diversity

interdependent components, so if key parts are removed, an entire ecosystem

Activity
may collapse and be lost. This c an happen if an environmental variable is

changed to be outside the range of tolerance of keystone species in an

Species have become extinct in

ecosystem. Eight c ategories of direct or indirect c ause of ecosystem loss are

all parts of the world. Research an

described here.

s
example in the area where you live.

1. Land-use change for agricultural expansion is the main cause of ecosystem loss.

s
In temperate zones, most areas suitable for farming were cleared of natural

forests, grasslands and wetlands before the 1970s. For example, the prairies

e
of North America were mostly plowed up in the 19th century. Since the 1970s,

it is mostly old-growth tropical forest ecosystems that have been lost.

r
2. Urbanization is another major c ause of land-use change and ecosystem

y
loss. The urban area of the world has doubled since 1992, to accommodate

the rapidly growing human population. Natural ecosystems have been

l
cleared to allow building of homes, oces and factories, together with the

n
associated infrastructure of roads and railways.

t
3. O verexploitation of natural resources has destroyed some ecosystems.

O
Gathering of fuel wood, hunting of animals for bushmeat and shing in

i
freshwater and marine habitats are examples. Even harvesting of a single

s
keystone species c an threaten ecosystems. An example is the overshing of

r
cod on the Grand Banks of Newfoundland. This is explored in Topic D4.2.

y
4. Mining and smelting destroy areas of natural ecosystems directly through
e

p
land-use change. In addition, pollution from these activities c an c ause much
v

more widespread damage. For example, nickel mining and smelting in

o
Ontario has c aused damage to lakes and rivers over a wide area by acid rain
i

and pollution of soils with copper, nickel and other metals. This has led to the
n

loss of natural forests.

C

5. Building of dams and extraction of water for irrigation c an lead to loss of

U

natural river and lake ecosystems. For example, the Colorado River now rarely
n

ows as far as the Pacic Ocean bec ause of water extraction for agricultural,

industrial and domestic uses. Similarly, the annual ooding of the Nile no

longer occurs bec ause a series of dams hold back water from monsoons in
o
d

Ethiopia.
i

6. Drainage or diversion of water for human uses has c aused the loss of
r

swamps and other wetlands in many parts of the world. For example, the
t
o

Mesopotamian M arshes in southern Iraq were drained by diversion of the

a

Tigris and Euphrates rivers in the 1990s. About two-thirds of the two million
f

hectares of these wetlands bec ame desert.

u
x

7. Leaching of fertilizers into rivers and lakes c auses eutrophic ation and algal

blooms. Oligotrophic ecosystems, in which organisms are adapted to low

l
O

nutrient concentrations, have been lost. L ake Erie for example has been
a

severely aected, with excessive growths of algae every summer since

the 1990s. Rivers c arry the nutrient-enriched water out to sea, where algal
v

blooms c an also occur.

E

8. Perhaps the most widespread threat to natural ecosystems is climate change.

Ecosystems are adapted to specic patterns of temperature, rainfall and

other physic al variables. When these variables change, entire ecosystems

c an be lost. Forest is replaced by scrubland or grassland if rainfall decreases.

Tundra is replaced by forest if temperatures rise. The relationship between

ecosystem types and climate is explored more fully in Theme B and the likely

future eects of climate change are considered in Theme D.

162
 Ecosystems

Two specic examples of ecosystem loss are described here but wherever you

live or attend school, there will be loc al examples that are worthy of study.

s
Mixed dipteroc arp forest of southeast Asia

s
The Dipteroc arpaceae is a family of about 700 tropic al as the peat in these areas c an be up to 15 m deep; this

e
rainforest trees. They are tall-growing and produce peat, formed over the past 4,000–5,000 years, c an store

valuable timber. Dipteroc arps used to dominate large 250tonnes of c arbon per hectare. Drainage during land

r
areas of rainforest in southeast Asia, including Brunei, conversion c auses the peat to decompose, releasing

Borneo and Papua New Guinea. CO into the atmosphere. This contributes to another
2

y
threat—rising sea levels c aused by global warming will
Mixed dipteroc arp forest (MDF) has an extremely high

ood deep-peat lowland areas with seawater, destroying

diversity of tree species. On the island of Brunei, for

l
what little MDF remains on such areas.
example, there are 20 native species of dipteroc arp and

n
small areas of MDF oen containing 10 or more of these

species. Interspecic hybrids may be produced but

O
they rarely grow to adult size. The highest diversity of

i
tree species tends to occur in areas with nutrient-poor

s
sandy soils.

MDF typic ally has particularly high quantities of

y
merchantable timber per hectare. As a result, it has
e
been widely targeted for logging, both legal and illegal.

p
Since the 1970s, most areas of MDF have been lost;
v

undisturbed areas are now largely found in upland sites

where access is more dicult.

o
i

The areas of MDF that have suered the greatest losses

n

are on lowland sites, especially where nutrient-rich soils

overlie deep peat. L arge areas have been converted

▴ Figure 13 Lowland mixed dipteroc arp forest, L ambir
U

to oil palm plantations. This is particularly unfortunate

Hills National Park, Borneo, M alaysia
n
o
d

Loss of the Aral Sea—an ecologic al disaster

i
r

The Aral Sea, between K azakhstan and Uzbekistan, was

t
o

the fourth largest lake in the world. It was fed by rivers but
a

it had no outows; instead, it lost water by evaporation.

f

As a result, it had higher salinity than a freshwater lake.

u

In the 1960s, two major rivers that fed the Aral Sea were
x

diverted to irrigate an area of desert. This led to falling

l

water levels and much of the former lake is now desert.

O

Apart from the reduction in the area and depth of the lake,

an increase in the water salinity was a major contributor

v

to ecosystem collapse. In some of the remaining parts of

the lake, the salinity has risen from 1% to more than 22%,
E

compared with about 3.5% for normal seawater. Twenty-

four species of sh were endemic to the Aral Sea, all of

which are now extinct. Most invertebrate species have

▴ Figure 14 A comparison of the Aral Sea in 1989 (le)

also disappeared.

and 2014 (right)

163
 Unity and diversity

A4.2.5 Evidence for a biodiversity crisis

Journalists use the term “biodiversity crisis” to describe the unprecedented losses

of ecosystems and species occurring today. As scientists, we must always look for

evidence before making a claim. In this c ase we need evidence of losses before

s
declaring that there is indeed a biodiversity crisis.

s
One source of evidence is the Intergovernmental Science-Policy Platform on

Biodiversity and Ecosystem Services (IPBES). This is an intergovernmental body

e
which assesses the state of biodiversity and periodic ally produces reports.

r
A more active approach is to gather evidence directly by monitoring. M any types

P
of variable c an be monitored:

y
• population size of a species—for example, the number of pairs of gannets in

l
a breeding colony each year

n
• range of a species—for example, the area over which rattlesnakes are found

in North Americ a

O
• diversity of species in an ecosystem—for example, the number of sh species

i
on a coral reef

s
• richness and evenness of biodiversity in an ecosystem—these are two

y
statistic al measures of diversity
e
• area occupied by an ecosystem, such as Brazilian rainforest

p
v

• extent of degradation of an ecosystem—for example, fragmentation of forests

o
on Brunei
i

• number of threatened species within a taxonomic group—for example,

n

native bird species of Hawaii

• genetic diversity within a species.

U

Although expert scientists play a key role in monitoring biodiversity and

identifying the most serious threats, there are opportunities for all citizens to
o

contribute. This is an example of what is oen c alled “citizen science”. Some

d

of the most useful data has been collected by individuals who have monitored
i

a population or an ecosystem regularly over many years. This c an allow the

r

detection of harmful changes while there is still time for them to be reversed.
t
o

a
f

Applying techniques: Use of Simpson’s diversity index

x

The Simpson’s reciprocal index quanties biodiversity by The highest values occur where there are equal numbers
l
O

taking into account species richness and evenness. The of individuals in the species present and there are many
a

greater the biodiversity in an area, the higher the value of D. species, so both evenness and richness are high.

The formula for Simpson’s reciprocal index of diversity is:

v

You could compare the diversity of species found in an

undisturbed forest with a clearing or glade in the same

N(N 1)

D =
E

forest undergoing succession. You could use a phone app

(∑ n(n 1)

such as Picture This or iNaturalist to identify the species of

where D = diversity index

individual plants.

N = total number of organisms of all species found

n = number of individuals of a particular species

164
 Ecosystems

Data-based questions: Using Simpson’s diversity index

Groups of students studied the species diversity of the beetle fauna found on

two upland sites in Europe. The same number of students searched for a similar

s
length of time in each of the two sites. The two sites were of equal area.

The number of individuals of the four species found at each site is given in

s
Table 1.

e
Species Site A Site B

r
Trichius fasciatus 10 20

P
Aphodius lapponum 5 10

y
Cicindela campestris 15 8

l
Stenus geniculatus 10 2

n
▴ Table 1

O
1. C alculate the reciproc al Simpson diversity index (D) for the beetle fauna

i
of the two sites. [3]

s
2. Suggest a possible conclusion that c an be formed. [2]

y
e

p
v

Activity

o
i

A population of silver-studded blue butteries (Plebejus methodology is used each year, to ensure the counts
n

argus) at Prees Heath in Shropshire, England is monitored are comparable. What variables would need to be

by loc al lepidopterists. The nearest other population of considered when recording numbers of butteries? Is

this species is about 100 km away. The graph in Figure 16 there a species in your area that could be monitored, to
U

shows counts of silver-studded blue butteries along a help in its conservation?

n

xed-route 5 m wide transect at Prees Heath. The same

o
d

1,600
tcesnart gnola dedrocer
seiflrettub fo rebmun

1,400
i
r

1,200
t

1,000
o

800

600
f

400
x

200
l

0
O

09 10 11 12 13 14 15 16 17 18 19 20
a

year
v

▴ Figure 15 Silver-studded blue buttery

▴ Figure 16
E

165
 Unity and diversity

Data-based questions: S atellite monitoring

Sentinel satellites are operated by the Europe an Space (b) Estimate the percentage of the land area that was

Agency (ESA). They provide images of e ach part of E arth burned in the 2019 dry season. [1]

s
every vedays. The data is made av ailable worldwide at
6. Suggest benets of satellite monitoring of burning

no charge and c an be used for monitoring changes to

and plowing [5]

s
land use.

e
The Sustainable Natural Resource M anagement

Association (SUNARMA) in Ethiopia uses these images to

r
monitor plowing and burning of vegetation.

The satellite images in Figures 17 and 18 show the same

y
area in dierent seasons. In the wet season, grassland

and arable crops in growth are light green and recently

l
plowed land is dark brown. In the dry season, grassland

n
and crops ready to harvest are light brown and recently

burned land is darker brown. Forest with trees in leaf is

t
▴ Figure 17 Dry season (11 November 2019)

O
darker green in both seasons.

i
The map in Figure 19 shows the same area as the satellite

s
images. It was produced by analysing the image for 11

r
November 2019 to identify areas that had been burned

y
during the dry season (brown) or were being burned
e
when the satellite passed over (purple). Green outlines

p
show designated forests managed by loc al community
v

cooperatives.

1. C alculate the size of the area shown in the satellite

o
i

images. [2]
n

▴ Figure 18 Wet season (2 August 2020)

2. Deduce what the state of the land is at these co-

ordinates: 900, 110 in the dry season; 910, 116 in the

U

wet season. [2]

n

3. Deduce what the designation is of land at 905, 116

13

and what the satellite images indic ate about its use.
o
d

[4]

12

4. Using the satellite images, suggest a hypothesis for

i
r

the distribution of forest. [2]

t
o

5. (a) State two signs of burning that are visible in the

11
a

dry season satellite image, with co-ordinates of

an example of each. [4]

f

▴ Figure 19 M ap with 1 × 1 kilometre grid squares

u
x

Applying technology to collect data

O

Th e A u du bo n So c i e ty s po n s o rs an annual b i rd count. You c an use the database to answer questions such as:

E ach ye a r in D e c e m be r, vo l u n t e e r bi rd - w a t c h e rs f ro m
v

a. Has the average latitude where a particular species is

a c ro ss No r t h A me r i c a re po r t s i g h ti n g s of b i rds . All of
observed shied northward due to climate change
E

th e s e s i g h t i n gs all e n t e re d i n to a s e a rc h a bl e da ta ba s e
over the past 40years?

(h ttp s : / / n e ta pp.a u d u b o n .o rg / c bc o b s e r v a t i o n / ). Th e

b. How has the presence in the Great L akes Region of

da t a b a s e contains re c o rd s f ro m m o re th a n 12 0 ye a rs of

the invasive and destructive emerald ash borer beetle

A u du bo n bi rd c o u n ts .

(Agrilus planipennis) impacted the population of birds

that feed on ash seeds / birds that feed on beetles /

birds that nest in dead trees?

166
 Ecosystems

Science as a shared endeavour

To be veriable, data usually has to come from a published source, which has

been peer-reviewed. This allows the methodology to be checked.

s
Consider the Audubon annual bird count as an example of data collected by

volunteer “citizen scientists”.

s
1. Discuss the strengths and limitations of data collected in this way.

e
2. Discuss the advantages and disadvantages of undertaking inquiries using

data collected by other people.

r
P

y
l
A4.2.6 Causes of the current biodiversity crisis

n
Humans have been c ausing species extinctions and loss of ecosystems for

thousands of years but a biodiversity crisis has developed since about 1970.

O
According to a UN report, by 2019, 75% of the terrestrial environment and 66%

i
of marine environments had been “severely altered” as a consequence of human

s
actions. Current rates of species extinction are between 100 and 1,000 times

higher than normal and they are rising. If this trend continues, the rate of species

y
loss could become 10,000 times higher than normal within the next 100 years.
e

p
The E arth’s four-billion-year history has been turbulent. During “Snowball E arth”
v

phases, the surface was almost completely covered by ice. However, there were

o
also phases when the entire surface was ice-free, even at the poles. At times,
i

there was a single giant continent; at other times, land was made up of many
n

isolated island continents. Five mass extinctions have occurred as a result of

unstoppable forces such as asteroid strikes, volc anic activity and transformations

in the atmosphere and climate patterns. Widespread ecosystem collapse has

U

unfolded over hundreds of thousands of years, or even longer. The current and
n

sixth mass extinction is happening much more rapidly. However, bec ause it is

largely c aused by human actions, it is stoppable.

o
d

To avert the biodiversity crisis, we must appreciate how human activities c ause

species extinction and ecosystem loss. The principal c auses, discussed in

i
r

Sections A4.2.3 and A4.2.4, are:

t
o

• hunting and other forms of over-exploitation

a
f

• urbanization, with towns and cities growing ever larger

u
x

• deforestation and clearance of land for agriculture, leading to loss of natural

habitats
l
O

• pollution of land and sea throughout the world

a

• spread of alien invasive species due to global transport or deliberate

v

introductions; such species may be pests, c ause disease or compete with

native species.
E

None of these c auses is new but their intensity has increased signic antly over

the last 100years. This is a consequence of the enormous rise in the number of

people on E arth. Between 1920 and 2020 the human population more than

quadrupled, from less than twobillion to almost eightbillion. O verpopulation is

the overarching issue that makes human activities a threat to most other species

and risks widespread ecosystem collapse.

167
 Unity and diversity

Data-based questions: Human population increases

Figure 20 shows estimated worldwide human population growth between 1700 and 2100.

12

s
2100
snoillib / noitalupop dlrow

s
10

2050

e
8

2019

r
6

1987

y
4

l
1928
1950

n
2

1803
1700

t
0

O
1700 1750 1800 1850 1900 1950 2000 2050 2100

i
year

s
▴ Figure 20

y
1. According to the graph, in what dec ade was there: 3. How many years did it take for the population to
e

p
double from:

a. the greatest absolute rise in the human

v

population [1] a. one to two billion [1]

b. the greatest percentage rise in the human b. two to four

o
billion [1]
i

population? [1]
n

c four billion to a predicted eight billion? [1]

2. a. In what year did the population reach

4. Using the data in the graph, discuss whether the rise

fourbillion? [1]
U

in the human population since 1700 has been:

n

b. When is the population predicted to reach

a. rapid [3]

eightbillion? [1]

b. exponential. [3]
o
d

5. Discuss what the peak human population might be,

i

assuming it does not continue to rise indenitely. [2]

r

t
o

A4.2.7 Need for several approaches to

f

u
x

conservation of biodiversity
l

The biodiversity crisis is acute and no single approach to tackling it will be

O

enough. Any strategy that c an help should be adopted, including all of those

described here.
v

In situ methods conserve species in their natural habitats. The ideal approach
E

is to leave areas of the E arth’s surface in a state of pristine wilderness. Partially

degraded pristine areas may still be extremely valuable for the purpose of nature

conservation. Legislation or land purchase c an be used to create national parks or

nature reserves. The larger the protected area, the better. Terrestrial, freshwater

and marine areas are now protected in many countries.

168
 Ecosystems

In situ conservation has some signic ant advantages. It ensures that a species

lives in the abiotic environment to which it is adapted, so it does not start to

adapt to dierent conditions. It allows the species to interact with other wild

species, conserving more aspects of the organism’s niche and the integrity of the

ecosystem. Animal behaviour patterns c an remain normal. In addition, costs are

s
low if a wildlife reserve is in a good enough state for human intervention to be

unnecessary.

s
e
Human inuences are so pervasive around the world that most areas of

wilderness are threatened with change. As a result, nature reserves oen require

r
active management. Depending on the type of ecosystem and the nature of

the threats, management may involve removal of alien species, reintroduction

y
of species that have become loc ally extinct, measures to increase or decrease

population sizes of herbivores and predators, prevention of poaching,

l
supplementary feeding of animals and control of access by humans.

n
In some c ases, ecosystems have become so damaged that major interventions

t
are needed. It is possible to reverse ecosystem collapse, and recovery is

O
sometimes surprisingly rapid. During the 21st century there has been an

i
increasing trend for rewilding, where degraded ecosystems are returned to as

s
natural a state as possible and balance is maintained by natural processes rather

r
than human intervention.

y
e
Ex situ conservation is the preservation of species outside their

p
natural habitats. At the outset, organisms are removed from the wild.
v

Traditionally, plant species were then grown in botanic gardens

and animals were kept in zoos. Clearly, it is not acceptable to

o
i

remove sc arce plants and animals from wild populations repeatedly.

n

Therefore, botanic gardens must propagate plants and zoos must

breed animals. Increasingly, zoos c arry out c arefully planned c aptive

U

breeding programmes, followed by release of the c aptive-bred

n

individuals back into their natural habitats.

In some c ases, removal and reloc ation of endangered species is

o
d

justiable bec ause they c annot safely remain in their natural habitats.

For example, populations of ightless native bird species in New

i
r

Zealand have been moved to oshore islands to protect them from

t

attacks by invasive alien predators. If the threat to a species in its

o

natural habitat is eliminated, the species c an be returned to its original

a

site. In New Zealand, this may happen if programmes to eliminate

▴ Figure 21 Takahē (Porphyrio hochstetteri) are

f

rats, stoats and possums are successful.

u

ightless birds that were presumed extinct for many

x

years. A small population was discovered in a remote

A more radic al approach to ex situ conservation is the long-term

valley on the South Island of New Zealand in the 1940s.

l

storage of living material that could be used for propagation in the

O

Since then, active conservation measures have increased

a

future. This material is c alled germplasm. The usual approach with

numbers by as much as 10% per year and there are now

plants is to store seed in seed banks at low temperatures, so they c an

more than 400 individuals. One of the conservation
v

maintain viability for long periods. With animals, the stored material
methods has been transloc ations to ve small predator-

may be samples of tissue, eggs or sperm.

free oshore islands
E

169
 Unity and diversity

s
s
e
r
P

y
l
y

n
t

O
i
s
▴ Figure 22 A new approach to conservation is to create “mainland islands” by fencing o

y
areas within which alien invasive species and other threats c an be controlled. The fence in

this photo is part of the boundary of Orokonui Ecosanctuary, a mainland island near Dunedin
e
in New Zealand

p
v

A4.2.8 Selection of evolutionarily distinct

o
i
n

and globally endangered species for

conservation prioritization in the EDGE of

U

Existence programme
n

The sc ale of the biodiversity crisis is so large that conservation eorts have to be

targeted where the benets are likely to be greatest. This raises the controversial
o
d

question of which species are most worthy of our eorts to conserve them. The

EDGE of Existence project uses two criteria to identify animal species that are
i
r

most deserving of conservation.

t
o

• Does the species have few or no close relatives, so it is a member of a very

a

small clade?
f

• Is the species in danger of extinction, bec ause all of its remaining populations
x

are threatened?
l
O

Lists are prepared of species that are both Evolutionarily Distinct and Globally
a

Endangered, hence the name of the project.

v

Species on these lists c an then be targeted for more intense conservation eorts

than other species that are either not threatened or that have close relatives.
E

Some species are the last members of a clade that has existed for tens or

hundreds of millions of years and it would be tragic for them to become extinct as

a result of human activities.

170
 Ecosystems

s
s
e
r
P

y
l
y

n
t

O
i
s
▴ Figure 23 Two species on the EDGE list: Loris tardigradus tardigradus (Horton

Plains slender loris) from Sri L anka and Bradypus pygmaeus (Pygmy three-toed sloth)

y
from Isla Escudo de Veraguas, a small island o the coast of Panama. What species on

EDGE lists are in your part of the world and what c an you do to help conserve them?
e

p
v

o
Global impact of science
i
n

Red wolves are native to parts of the southeastern US Endangered Species Act and therefore given legal

United States. They are intermediate in form between protection. The International Union for the Conservation

grey wolves (Canis lupus) and coyotes (Canis latrans). of Nature (IUCN) also lists it as a critic ally endangered
U

There has been disagreement whether to classify red species. However, it is not listed in the appendices of the
n

wolves as a subspecies of wolf (Canis lupus rufus) or Convention on Trade in Endangered Species (CITES).

as a distinct species (Canis rufus). Bec ause of this, it is Some of the debate is based on the lack of a universally
o
d

sometimes excluded from endangered species lists accepted species concept.

despite its critic ally low numbers. It is listed under the

i
r

t
o

a
f

u
x

l
O

a
v
E

▴ Figure 24 Red wolf (le) and coyote (right). If red wolves are as similar to coyotes as to grey wolves,

should they be classied as a separate species or a subspecies of grey wolf ?

171
 Unity and diversity

ATL Thinking skills: Evaluating and defending ethic al positions

When evaluating an ethic al question, dierent criteria c an Smallpox viruses (Variola major and Variola minor)

yield dierent results. Consequentialism uses the standard

The disease smallpox was c aused by two types of virus,

s
that “the ends justify the means”; motivism uses the

Variola major and Variola minor. It c aused the deaths of

standard that understanding the intentions of an action is

hundreds of millions of people. Smallpox vaccines were

s
important in evaluating whether it is ethic al.

introduced to give immunity to the disease. In 1967,

e
Issues such as which species should be prioritized for
the World Health Organization started a c ampaign to

conservation eorts have complex ethical, environmental,

eliminate the disease completely by vaccination. The

r
political, social, cultural and economic implications and
last c ase of smallpox was in 1978. Bec ause there are no

therefore need to be debated. Of the 85,604 species

reservoirs of the viruses that c ause the disease, it has been

y
identied in the IUCN Global Red List, 24,307 are
permanently eradic ated.

classied as threatened with extinction. Resources to

The extinction of a virus that c auses death and suering

l
address this challenge are limited and priorities have to be

y
in humans is uncontroversial. But should humans try to

n
set. However, conicts of values can arise. Dierent groups

eradic ate other groups of troublesome organisms—for

will have dierent goals—such as defending against the

t
example, bacterial pathogens, parasites of the human gut

O
most predictable species losses; maximizing phylogenetic

or skin, or pests or diseases of crop plants or livestock?

i
diversity; conserving keystone species over others; or

These issues raise important ethic al questions. Do we

s
conserving species of cultural signicance—and dierent

as humans have the right to eliminate species that are

goals will necessitate dierent approaches.

r
harmful—or simply not useful—to us?

y
e

p
v

o
Linking questions
i
n

1. In what ways is diversity a property of life at all levels of biologic al

organization?
U

a. Distinguish between prokaryotic cells and eukaryotic cells.

n

(A2.2.5 and A2.2.6)

b. Outline the mechanism of adaptive radiation. (A4.1.9; HL)

o
d

c. Explain how DNA is able to code for an innite variety of proteins.

(A1.2.9)
i
r

2. How does variation contribute to the stability of ecologic al communities?

o

a. Outline the concept of niche. (B4.2.1)

f

b. With reference to named examples, construct an annotated food

u

web. (C4.2.4)
x

c. With reference to ecologic al succession, distinguish between the

l
O

structure of a pioneer and climax community. (D4.2.12)

a
v
E

172
 Ecosystems

TOK

In what ways do values aect the

s
s
production and acquisition of

e
knowledge?

r
P

y
Individuals have dierent opinions about what is important, hypothesis testing:

useful or worthy of attention: they have dierent values.

1. An experimenter c an mistakenly reject the null

l
Science is a human endeavour, so it is not surprising that

hypothesis when it is true. In medic al testing, this would

n
scientists have dierent approaches to decision making.

be known as a false positive. This is a type I error.

t
Research funding is limited and the costs of scientic
2. An experimenter c an accept the null hypothesis when it

O
research are oen met by grant agencies. But who decides

i
is false. This is a type II error or a false negative.

how funds are alloc ated? Scientists submit research

s
proposals to agencies and each applic ation is reviewed by
It is not possible to minimize the likelihood of one type

r
a funding panel. Some grant applic ations ask scientists to
of error without increasing the likelihood of the other

y
project outcomes or suggest applic ations of the research
type of error. This choice involves a value judgement. For
e
before it has even begun. Q uestions arise when the grant

p
example, the null hypothesis might say that an introduced

agency has a stake in the study’s outcome. A sponsor may

species does not have an eect on the host community.
v

fund several dierent research groups, suppressing results

To minimize the risk of a type I error, the researcher might

that run counter to their interests and publishing those

invest signic antly
o in controlling the invader when it would
i

that support their industry. For example, in a 2008 report

not have become invasive. On the other hand, minimizing
n

based on chemic al industry studies, the US Food and

a type II error might lead them to ignore the threats

Drug Administration (FDA) concluded that the bisphenol

represented by the invader. Their choice will be based on a
U

A (BPA) found in plastic containers was not a health

value judgement.
n

risk. Independent research studies reported dierent

conclusions. There have been claims of funding bias in many Perhaps the most widely discussed false positives in

areas, including pharmaceutic al research, nutrition research medical screening come from the breast cancer screening
o
d

and climate change research. procedure known as a mammogram (Figure 1). The US

rate of false positive mammograms is the highest in the

i
r

According to the UN World Health Organization, there

world; one study found it to be as high as 15%. Women are
t

are 20 neglected tropic al diseases (NTDs). These diverse

o

oered mammograms annually, starting in middle age. The

a

conditions are common in tropic al areas, mostly aecting

consequence of the high false positive rate in the US is that,

poor communities and disproportionately aecting

f

in any 10-year period, half of the American women screened

u

children and women. M any of the diseases have aected

receive at least one false positive mammogram. False
x

humanity since ancient times. It has been stated that these

positive mammograms oen result in costly follow-up tests.

diseases are under-researched and eorts to eradic ate

l

They also cause women unnecessary anxiety. In contrast, the

O

them are under-funded, bec ause the values of the research

a

Netherlands has the lowest rate in the world, with just 1%

community lead to prioritization of other diseases.

false positives being reported. The lowest rates are generally
v

in Northern Europe where mammography lms are read

In scientic investigations, scientists have to choose

twice and there are high thresholds for additional testing.

between hypotheses. Inevitably, these choices are

E

When contrasting the two jurisdictions, what dierences in

inuenced by human values such as a desire for simplicity,

values are evident?

accuracy of data and explanatory power. In statistic al

testing, researchers test null and alternative hypotheses.

One standard for making judgements is known as Occ am’s

The null hypothesis is a hypothesis that a given factor

R azor. In everyday language, this is the idea that the simplest

has no observable eect. Two types of error c an occur in

explanation or more probable c ause is most likely to be

173
 Unity and diversity

true. In cladistics, a characteristic shared between two

groups c an indic ate a shared ancestry. Alternatively, it could

indic ate that the characteristic has evolved twice. It is less

likely that complex traits evolved twice or multiple times, so

the criterion for judgement when constructing cladograms

s
is parsimony—the history with the smallest number of rare

events is assumed to be the most likely. This is not always the

s
c ase; for example, the octopus eye and the vertebrate eye

e
are remarkably similar but the consensus is that they evolved

separately. Similarly, warm-bloodedness in birds and

r
mammals is believed to have evolved separately. In general,

however, the simplest theory is oen true.

y
In medic al diagnosis, an aphorism is: “If you hear the

l
sound of hooves, it could be zebras, but it is most likely

n
horses”. The most rational approach is to start with the

most likely scenario and progress toward rarer conditions.

t
S adly, extreme risk avoidance or prot motivation c an lead

O
i
practitioners to start with the least likely but worst c ase

s
hypothesis and test towards the more likely explanation.

y
Onchocerciasis is known as river blindness. It is a disease

c aused by infection with the parasitic worm Onchocerca

e

p
volvulus. It is one of the 20 neglected diseases as no
v

vaccination is available despite the disease aecting

o
humanity since ancient times. Figure 2 shows the parasite
i

coming out of the antenna of an adult black y. The black y

▴ Figure 1 A woman having a mammogram

is a vector for the disease.

n

C
U

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

▴ Figure 2 Onchocerca volvulus parasite coming out of the antenna of a black y

174
 Ecosystems

End of chapter questions

1. About 2.5 million years ago, falling sea levels resulted c. Using the data from ninemillion years ago and the

in the joining together of North Americ a and South present, c alculate the percentage increase in the

s
Americ a through a narrow land bridge, the isthmus total number of genera found in South Americ a. [1]

s
of Panama. This event allowed two-way traffic of land

d. Discuss why the percentage increase in genera

mammals between the formerly isolated continents.

is much greater than the apparent percentage

e
A redistribution of families and genera (plural form for

increase in families. [2]

genus) occurred. The graphs in Figure 1 show the total

r
e. State a form of evidence on which the data in the
number of known native and immigrant families and

graphs is based. [1]

P
genera in South Americ a over a time span ranging from

y
ninemillion years ago to the present.
f. Referring to the competitive exclusion principle,

l
suggest why the number of native families and
a. Compare the changes in the number of South

n
genera declined. [2]
Americ an native families and the number of North

Americ an immigrant families in the onemillion years

g. M any of the immigrant mammals were placental

t
after the formation of the land bridge. [1]

O
mammals and a number of the native mammals

i
were marsupials. Suggest what is the adaptive
b. Suggest a reason for the decline in the number of

s
advantage of placental rather than marsupial
South Americ an native families and the number of

gestation. [2]
North Americ an immigrant families within the last

y
1.5million years. [1]
h. With reference to this example, outline the
e

p
concept of adaptive radiation. [3]
v

South America

Number of families
o
Number of genera
i

10 20 30 0 20 50 100 150
n

Present

1
U

2
oga sraey fo snoillim

3
o
d

5
i
r


t
o


a


f


x

South American native families

l
O

North American immigrant families

a

Source: Marshall. 12. Science. ol. 215. P 1351–135.

v

▴ Figure 1
E

175
 Unity and diversity

2. The mountain yellow-legged frog (Rana muscosa) d. The “without trout” group was achieved by the

was once a common inhabitant of the Sierra Nevada intentional removal of trout from the experimental

(C alifornia, USA). It has declined during the past century waterways. Discuss the challenges of such a

due in part to the introduction of non-native fish, such conservation measure. [2]

as trout, into naturally fish-free habitats. The bar chart

e. O utline a method that could be used to determine

s
in Figure 2 shows the average number per lake of

the population of frogs in the lake. [3]

tadpoles.

s
In order to restore the frog population, introduced trout

a. State the number of tadpoles per lake with and

e
were removed from the lakes. The map of the LeConte

without trout. [1]

Basin study area shows the distribution of mountain

r
b. Compare and contrast results for lakes with and yellow-legged frogs and trout populations just prior to

without trout. [2] the removal of the trout in 2001. The graphs show the

y
population of tadpoles and frogs in the lakes before,

c. The trout might affect the number of frogs or

during, and after the removal of the trout.

l
tadpoles by competing for resources. Suggest one

y
other way in which trout might affect the number of

n
tadpoles or frogs in lakes. [1]

O
i
1,000

s
Key

800

Lake status
ekal rep

y
600 with trout
e

p
400 without trout
rebmun

200

o
i
latot

20
n

15

10
U

Source:  reenbur 2004 PNAS ol 101 p 646650

opyriht 2004 ational caemy o Sciences S

5
n

0
o
d

▴ Figure 2
i
r

t
o

3. One challenge associated with establishing nature b. With respect to the example of disturbance-
f

reserves is concerns about “edge effects”. The graph in adapted beetles, suggest what is meant by an
u

Figure 3 shows that some edge effects in the Amazon indic ator species. [2]
x

rainforest are detected quite far in from the edge.

c. Explain how this information about edge effects c an

l
O

a. Determine how far from the forest edge an increase influence the design of reserves. [3]
a

in disturbance-adapted beetles would be detected.

[1]
v
E

176
 Ecosystems

Key

Lae

0 0.25

no trout tadpole or ro

m

no trout tadpole and

ro preent

s
trout preent

s
no tadpole or ro

pper

trout tadpole and ro

e
Leonte Lae

preent

Stream

r
trout aent

y
trout preent

natural arrer to trout

Lower

l
movement

y
Leonte Lae

n
t
250 pper Leonte Lae Key

O
enlero

50
tadpole

i
enlero
200
ro

40

s
150
trout
30
1–

y
removed
m

1–

100
20
m
01

e
01

p
50
remun  ytned

10
remun  ytned
v

0 0

o
Lower Leonte Lae
10
30
i


n

20


trout
 e l opd a t

 o r

removed
4

10
n

2
o
d

0 0


5
0


0
0


0
2
1

i
r

Source: Knapp et al. 2007.

year
◂ Figure 3
t
o

a
f

ncreased tree mortalit

u
x

ncrease in presence o disturanceadapted utterflies

tceffe

ncrease in presence o disturanceadapted eetles

O

ecrease in species ricness o lealitter communit

e gd e

ncrease in presence o disturanceadapted trees

v

ecrease in presence o understoradapted irds

ncrease in presence o disturanceadapted understor plants

E

0 100 200 00 400 00

edge penetration distance / m

Source: WF L aurance. 2008. Biological Conservation. Vol. 141. Pp. 11–144.

▴ Figure 4

177
 B Fo r m and function

s
s
1 Molecules

e
r
The form of a molecule r e f e rs to its shape and underlying

P
s t r u c t u re. Biologic al molecules are based on c arbon.

y
C arbon c an form four bonds. It c an form s i n g l e, double

l
and triple bonds. It c an form cov alent and polar cov alent

n
bonds. It c an form rings and chains. Living things

t
depend on the s t r u c t u ra l d i v e rs i t y of molecules that c an

O
i
be built with c arbon backbones.

s
Ad a p t a t i o n s are forms that correspond to function.

y
These adaptations p e rs i s t f rom g e n e ra t i o n to g e n e ra t i o n
e
bec ause they inc re ase the chances of surviv al to

p
v

reproductive a g e. The molecules produce d by living

o
organisms are used for metabolism, d e f e n s e, pre dation
i

and a ra n g e of other functions. Their functions are

n

dependent on their unique forms.

U

Ve n o m f rom the black mamba contains the

n

molecule fasciculin which binds to the enzyme

a c e t y l c h o l i n e s t e ra s e preventing it f ro m bre aking d ow n

o
d

acetylcholine in the sy n a p s e of nerves. This c auses

i

i nv o l u n t a r y muscle c o n t ra c t i o n s which immobilizes the

r

p r e y. The b a c k g ro u n d image s h ows fasciculin ( p u r p l e)

o

binding to asite on the e n z y m e.

f

u
x

l
O

a
v
E
B1.1 C arbohydrates and lipids

In what ways do variations in form allow diversity of function in c arbohydrates and lipids?

s
C arbohydrates and lipids are both composed of c arbon, oxygen and hydrogen. However, they have very dierent

s
properties bec ause of dierences in the form of their molecules. A total of 1,679 dierent molecules with a wide

e
range of properties have been identied in watermelon plants. Figures 1 and 2 show some examples of both types of

molecules. Compare and contrast the relative amounts of oxygen, c arbon and hydrogen in c arbohydrates and lipids.

r
Why are lipids relatively insoluble in water compared to c arbohydrates?

OH

y
O

OH
HO
H N
2
OH

l
O NH
2
HO

y
OH

n
OH

HO HO
O

HO
O
OH

t
O O OH

O O

O
O

i
HO O
OH

s
HO OH

NH OH
2
HO

r
OH

y
raffinose chitotriose
e

p
▴ Figure 1 Some sugars
v

o
How do c arbohydrates and lipids compare as energy storage compounds?
i
n

O
nervonic acid
C arbohydrates in the form of starch or glycogen and lipids

in the form of fats or oils c an be used as energy stores. They

OH
U

are chemic ally stable and energy is released when they are

O
arachidic acid
n

oxidized by cell respiration. How does the relative amount

of oxygen in the molecule aect how much energy per

OH

gram it releases? What advantages do fats and oils have as

o
d

energy sources? What advantages do c arbohydrates have? O

12, 13(S)-epoxylinolenate

C an both c arbohydrates and lipids be used in either aerobic

i
r

OH
or anaerobic respiration? Which energy form is more easily
t

transported from one part of an organism toanother?

o

▴ Figure 2 Some fatty acids

f

SL and HL
x

B1.1.1 Chemic al properties of a c arbon atom allowing for the formation of diverse compounds upon which life isbased
l

B1.1.2 Production of macromolecules by condensation reactions that link monomers to form a polymer
O

B1.1.3 Digestion of polymers into monomers by hydrolysisreactions

a

B1.1.4 Form and function of monosaccharides

v

B1.1.5 Polysaccharides as energy storage compounds

B1.1.6 Structure of cellulose related to its function as a structural polysaccharide in plants

E

B1.1.7 Role of glycoproteins in cell–cell recognition

B1.1.8 Hydrophobic properties of lipids

B1.1.9 Formation of triglycerides and phospholipids by condensation reactions

B1.1.10 Dierence between saturated, monounsaturated and polyunsaturated fatty acids

B1.1.11 Triglycerides in adipose tissues for energy storage and thermal insulation

B1.1.12 Formation of phospholipid bilayers as a consequence of the hydrophobic and hydrophilicregions

B1.1.13 Ability of non-polar steroids to pass through the phospholipid bilayer

179
 Form and function

nucleus with six protons and

B1.1.1 Chemic al properties of a c arbon

six, seven or eight neutrons

atom allowing for the formation of diverse

compounds upon which life is based

s
C arbon is only the 15th most abundant element on E arth, but without it life would

not exist. Its chemic al properties allow many dierent forms of molecule to be

s
produced, so the range of functions is almost limitless.

e
+

+ C arbon atoms c an form covalent bonds with other atoms. A covalent

+

r
bond is formed by sharing a pair of electrons between two adjacent atoms.
+
+

Thenegatively charged shared electrons are attracted to the positively charged

y
nuclei of both atoms. Covalent bonds are the strongest type of bond between

atoms. This means stable molecules based on c arbon c an be produced.

l
y
E ach c arbon atom c an form four covalent bonds, so molecules containing

n
c arbon c an have complex structures. There c an be four single covalent bonds or

t
two single and one double covalent bond. Double covalent bonds are found, for

O
six electrons with four of
example, in unsaturated fatty acids.

i
them in the outer shell

s
C arbon atoms c an form covalent bonds with other c arbon atoms or with atoms

▴ Figure 3 Stylized drawing of a

of other elements such as hydrogen, oxygen, nitrogen or phosphorus. C arbon

y
c arbon atom

atoms c an bond with four atoms of one other element — for example, with four
e
hydrogen atoms to form methane. They c an also bond to more than one other

p
element — for example, with oxygen and hydrogen to form ethanol.
v

o
C arbon atoms c an be linked up by covalent bonds to form a chain of any length.
i

F atty acids contain unbranched chains of up to 20 c arbon atoms. Chains c an also

n

be branched, with the branch oen made using an oxygen atom.

Single covalent bonds allow both of the bonded atoms to rotate, but not to move
U

further apart or nearer to each other. The covalent bonds formed by a c arbon
n

atom spread apart as much as possible so they form a tetrahedral shape. So, a

chain of covalently bonded c arbon atoms is not straight — the straightest it c an be

is a zig-zag. Bec ause

o

of the bond angles, chains of c arbon atoms c an form rings.

d

The ring may be made entirely of c arbon atoms — for example, in menthol which

is synthesized by mint plants. Or contain an atom of another element, usually

i
r

oxygen or nitrogen. A molecule may contain a single ring as in the base thymine,
t
o

a
f

u
x

l
O

a
v
E

▴ Figure 4 The plant Chrysanthemum cinerariifolium produces chrysanthemic acid, a very

unusual molecule that has a ring of three c arbon atoms. You could research the reasons for

this molecule being rather unstable and the benets to the plant of producing it

180
 Molecules

or two rings as in adenine, or more. Cholesterol molecules have four rings all

composed entirely of c arbon.

methane — a single carbon N

H
with four single covalent

s
H C N
bonds all to hydrogen

s
H H
C C

e
N N
ethanol — two carbon H

H C H
atoms and bonds to two
H

r
different other elements adenine — with two rings both

H H

P
with carbons and nitrogens and

y
sharing of electrons in the ring
H

O
ethanoic acid — single

l
H C C covalent bonds and

n
O H one double bond

O
i
H H H H H H H H H H H H H H H H H

s
O

H C C C C C C C C C C C C C C C C C C

y
OH

H H H H H H H H H H H
e

p
linolenic acid — an omega-3 fatty acid with a

chain of 18 carbon atoms containing 3 double bonds

v

o
▴ Figure 5 Some common naturally occurring c arbon compounds
i
n

Activity: M acromolecules
U

Titin is a giant protein that acts as a molecular spring in muscle. The backbone
n

of the titin molecule is a chain of 100,000 atoms, linked by single covalent

bonds. C an you nd an example of a molecule in your body with a chain of

o
d

over 1,000,000,000 atoms?

i
r

Science as a shared endeavour: SI units

o

The International System of Units (SI) is the scheme for metric units of measurement, agreed by scientists around the
f

world in 1960. From time to time it is updated. There are 7 base units and 22 other units derived from the base units.
u
x

E ach unit c an be given prexes that make it larger or smaller. The preferred prexes change the size by a factor of a

thousand but the prex “centi” is still sometimes used to indic ate a hundredth.
l
O

Base units Examples of derived units Metric prexes

2 9

• second (s) time • newton (N) force (kg m s ) • giga (G) 10 (billion)
v

1 6

• metre (m) length • hertz (Hz) frequency (s ) • mega (M) 10 (million)

2 3
E

• kilogram (kg) mass • pasc al (Pa) pressure (N m ) • kilo (k) 10 (thousand)

• ampere (A) electric current • joule ( J) energy (N m) • milli (m) 10 (thousandth)

1 6

• kelvin (K) temperature • watt (W) power (J s ) • micro 10 (millionth)

1 9

• mole (mol) amount of substance • volt (V) voltage (W A ) • nano 10 (billionth)

2 12

• c andela (cd) luminous intensity • lux (lx) illuminance (cd m ) • pico 10 (trillionth)

181
 Form and function

B1.1.2 Production of macromolecules by

condensation reactions that link monomers

to form a polymer

s
M acromolecules are molecules composed of a very large number of atoms,

with a relative molecular mass above 10,000 atomic mass units. The main classes

s
of macromolecule in living organisms are polysaccharides, polypeptides and

e
nucleic acids. E ach of these is made by linking together subunits into a chain.

The subunits are monomers and the chain is a polymer. In each c ase, the

r
chemic al process that links another monomer onto the end of the polymer is a

condensation reaction.

y
In a condensation reaction, two molecules are linked together and at the same time a

l
smaller molecule is released. When polysaccharides, polypeptides and nucleic acids

n
are constructed, the simpler molecule is always water. It is produced by removing a

hydroxyl group (–OH) from one of the molecules being linked and a hydrogen from

t
the other. This allows a bond to be made to bridge the two molecules.

O
i
H

s
OH HO OH N

y
e
H

p
HO OH N
v

o
H O
2
H O
2
i

▸ Figure 6 Two methods of linking a

n

monomer to a polymer by a condensation O N

reaction
U

Energy is required to construct polysaccharides, polypeptides and nucleic

n

acids by condensation. This energy is supplied by ATP. The synthesis of

polysaccharides is described in detail here. Polypeptide synthesis is described in

o
d

Topic B1.2 and nucleic acid production in Topic A1.2.

A disaccharide is two monosaccharides linked together. A polysaccharide is a

6
CH OH
2
i
r

chain of monosaccharides. Glucose is the monosaccharide used to make the

t

5 C O
polysaccharides glycogen, starchand cellulose.
o

H or OH
H
a

H
Glucose molecules are linked up with glycosidic bonds. These are C–O–C

4C 1C
f

OH H
linkages formed by condensation, using hydroxyl groups. The hydroxyl on C
1
u

HO OH or H
of a glucose is linked to the hydroxyl on C at the end of the growing chain.
x

3 C C
2

In an unbranched chain, all the glycosidic bonds are 1→4. To form branches,
l

H OH the C of a glucose is linked to theC of a glucose already in the chain. This

O

1 6
a

1→6 linkage forms a side-branch, and more glucose molecules c an be added

▴ Figure 7 Structure of glucose. There is always

to it with1→4 bonds.

one –OH (hydroxyl) group and one –H group on

v

C . The upper group is –H in α-glucose and –OH

1

Cellulose molecules in plant cell walls are unbranched chains of β glucose

in β-glucose
E

that c an contain 15,000 or more glucose molecules. Glycogen molecules

in liver or muscles cells are branched chains of α glucose, with up to 60,000

glucosemolecules.

182
 Molecules

H H H H

monosaccharides, C H O
6 12 6

e.g. glucose, fructose, galactose

OH

s
condensation hydrolysis
H O
2

s
(water removed) (water added)

e
disaccharide, C H O

r
12 22 11

e.g. maltose, sucrose, lactose

P
HO OH

y
O

bond

H O
2

l
y
+ OH

n
condensation hydrolysis

t
O

O
H H

i
olysaccharide

s
e.g. starch, glycogen

HO O O O OH

r
OH HO

y
▴ Figure 8 Formation of 1–4 glycosidic bonds by condensation and their breakage
e
byhydrolysis
▴

p
Figure 9 In a hydrolysis reaction, water

molecules are split to provide hydrogen

v

and hydroxyl groups. These are used to

o
B1.1.3 Digestion of polymers into monomers
make bonds to replace the bond that has
i

beenbroken

by hydrolysis reactions
n

Polymers are deconstructed so the monomers in them c an be reused to

build new polymers or used as a source of energy. Hydrolysis reactions are

5 CH OH
U

used to deconstruct polysaccharides, polypeptides and nucleic acids into O

n

OH

monosaccharides, amino acids and nucleotides. These are the reactions that 4
C C1
H H

occur during digestion. H

H
o
d

3 C C2

Digestion of polysaccharides, polypeptides and nucleic acids can be carried out by

i

all cells. Digestion also happens outside the cell in the gut of animals. Decomposers OH OH
r

ribose — a pentose

release digestive enzymes into the environment around them in order to break down
t
o

6 CH OH
polymers by hydrolysis so they can absorb and use themonomers. 2
a

5
C O
f

H H
u

H
x

4
C C
1

OH H

B1.1.4 Form and function of

HO OH

C C2
l

monosaccharides
O

H OH
Monosaccharides have between three and seven c arbon atoms. Pentoses have

glucose — a hexose
v

ve c arbons and hexoses have six. Both pentoses and hexoses normally have

molecules with a ring of atoms. There is one oxygen atom in the ring and four or

CH
6 OH
2
E

ve c arbon atoms.

O
OH

C
5 C2
Monosaccharides have properties that allow them to be used in a variety of ways
H H

H
by living organisms. Glucose is a widely used monosaccharide. 1 CH OH
2

4 C C3

OH OH
fructose — a hexose

▴ Figure 10

183
 Form and function

Use of molecular models: Modelling glucose

Pentoses and hexoses are unusual in that they c an exist to be in the ring form in order to form disaccharides and

in straight-chain form as well as in ring form. They need polysaccharides.

s
H O

1 C
6
6

s
CH OH CH OH
2 2

e
5
H H H 5 H

C OH O

HO 4 H H

r
4
1

C C

OH H OH H
1

P
H

y
C C 3
2

3 2

HO HO OH

H C OH

l
H OH
H OH

n
CH OH
2

structure A structure B structure C

O
▴ Figure 11

i
1. Using a molecule model kit, construct a model of 4. Attach carbon 1 to the oxygen on carbon 5 and reposition

s
structure A. This is the straight-chain form. the detached hydrogen as shown in structure C.

r
2. Twist the model so that c arbon 1 comes near the 5. Place the model on a table. Identify the plane of the

y
oxygen attached to c arbon 5 as shown in structure B. ring. Which –OH groups are above the plane of the
e

p
ring and which are below it?
3. Break the double bond on carbon 1 and remove the

hydrogen attached to the oxygen attached to carbon 5. 6. Is your model α-glucose or β-glucose?
v

o
i

Data-based questions: Health consequences of the consumption of fructose

n

Obesity (excessive weight) is recognized as a global health problem and has been correlated with a large number of
U

health issues, diseases and deaths. The increased consumption of fructose, now widely used as a sweetener, has been
n

associated with the increase in obesity.

In a study, mice were divided into four groups. E ach group was given the same amount of food and either a so drink
o
d

with a dierent sweetener or water.

1. Distinguish between the structure of sucrose and fructose. [1]

i
r

2. Use the graph in Figure 12 to compare and contrast the body fat accumulation in the four groups of mice. [3]
t
o

so drink wit fructose

a

8
so drink wit sucrose
g / n o it a l um u c c a

gnicudorp-esobir otni

diet drink wit artificial sweetener

u

water 30
stinu
x

25
yratibra / yawhtap
l
O

4
a

20
t af

15
v
yd ob

10
ekatpu
E

5
0

0 10 20 30 40 50 60 70 glucose fructose

time / days

▴ Figure 12 Body fat accumulation in four groups of mice ▴ Figure 13 Uptake of sugars in pancreatic cells

184
 Molecules

Studies investigated the role of glucose and fructose in the development of pancreatic c ancer cells. Pancreatic c ancer

cells were grown in equal concentrations of each sugar and the uptake of each into ribose-producing pathways was

measured. The graph in Figure 13 shows the range of uptake of sugars and the mean value.

3. Discuss if the results provide clear evidence of a dierence in uptake of the two sugars. [2]

s
4. Determine which sugar is primarily used in the production of ribose by pancreatic c ancer cells. [1]

s
e
Properties and uses of glucose

• Like all monosaccharides, glucose is soluble and is a relatively small molecule,

r
so it is easily transported. It circulates in blood, dissolved in the plasma.

y
• Like most other c arbohydrates, glucose is chemic ally very stable. This

property is useful for food storage. However, glucose would c ause osmotic

l
problems if it was stored in cells in large quantities. Therefore, it is usually

n
converted to glycogen or starch.

t
• Glucose yields energy when it is oxidized. It c an therefore be used as a

O
substrate forrespiration.

i
s
▴ Figure 14 A black bear is feeding on

B1.1.5 Polysaccharides as energy storage

wild berries. Foods containing glucose

y
are attractive to animals bec ause of their

compounds

energy yield, so plants put glucose (and

e
Starch and glycogen are used as energy stores. Starch is used in plants and glycogen

p
usually alsofructose) in the esh of animal-

in animals. Both of these substances are composed of large numbers of α-glucose dispersed fruits and in the nectar of animal-
v

pollinated owers
molecules, which can be used a substrate in aerobic and anaerobic cell respiration.

o
i

There are two types of starch molecule.

n

• Amylose is an unbranched chain of α-glucose linked by 1→4 glycosidic

bonds. Bec ause of the bond angles, the chain is helic al rather than straight.
U

• Amylopectin has the same structure as amylose but there are some 1→6
n

glycosidic bonds making the molecule branched.

CH OH
2
o
d

OH
i

H
r

2
t

C
o

O
a

OH
H

O
f

O
u

CH
2
x

O
O
C
H
l

2 O
OH
H
H
O

2
a

H O O
C O O H

O
v

H OH

O
E

O O
H H

O CH OH
2
O
H

H
O
O

▴ Figure 15 Small portion of an amylopectin molecule showing six α-glucose molecules,

all linked by 1→4 bonds apart from one 1→6 bond that creates a branch

185
 Form and function

Glucose c an be removed from starch and glycogen molecules when it is needed.

A hydrolysis reaction breaks a 1→4 glycosidic bond to separate one glucose

molecule from the end of a chain. This allows it to be transported elsewhere or

used in the cell. You c an think of starch and glycogen as a sort of bank account

bec ause glucose c an be deposited when there is a surplus and withdrawn when

s
there is a shortage. Adding or removing glucose c an happen more quickly with

amylopectin than amylose bec ause the branched structure provides more ends

s
of chains.

e
Glycogen has a similar structure to amylopectin: α-glucose molecules linked

r
by 1→4 glycosidic bonds and branched by 1→6 bonding. In glycogen, about

1 in 10 glucose molecules has a 1→6 bond, compared with about 1 in 20 in

y
amylopectin, so glycogen molecules are more branched.

l
Glycogen c an contain tens of thousands of glucose subunits and amylopectin

y
c an contain more than a hundred thousand. The very large size of these

n
molecules gives them much lower solubility than glucose, so they contribute little

t
to the osmotic concentration of cells. This means starch or glycogen c an be used

O
to store large amounts of glucose without the cell swelling up with water drawn

i
in by osmosis. The branched structure of glycogen and amylopectin makes them

s
relatively compact despite their huge molecular mass. This is another useful

r
property in a storage compound.

y
e
A consequence of the limitless addition and removal of glucose is that starch and

p
glucose do not have a xed molecular mass, so molar solutions c annot be made.
v

Concentrations have to be expressed in percentage terms (grams of substance

o
3

per 100 cm of solution).

i
n

B1.1.6 Structure of cellulose related to

U

its function as a structural polysaccharide

inplants
o
d

Cellulose, like starch and glycogen, is composed of glucose, but its properties

are markedly dierent bec ause it is a polymer of β-glucose rather than α-glucose.
i
r

Condensation reactions link C on a free β-glucose molecule to C on the

1 4
t
o

β-glucose at the end of the growing cellulose molecule. All the links in cellulose
a

are 1→4 glycosidic bonds, so it is an unbranched chain. A cellulose molecule c an

contain more than 10,000 β-glucose molecules each with a size of about 1 nm,
f

giving an overall length of more than 10 µm.

x

In β-glucose, the –OH group on C is angled upwards and the –OH group
l

1
O

on C is angled downwards. To bring these –OH groups together and allow

a

a condensation reaction to occur, each β-glucose added to the chain has to

be inverted in relation to the previous one. The glucose subunits in the chain
v

therefore face alternately upwards and downwards.

E

CH OH CH OH H OH
CH OH 2
2 2

H OH H O OH H O OH H H
O

OH H
OH H OH H OH H

▸ Figure 16 Beta glucose molecules c an

O
HO H HO H HO H H OH

only form a 1→4 glycosidic bond if one

faces up and the other faces down H OH H OH H OH CH OH

2

186
 Molecules

The chains of α-glucose in starch wind into a helix, but in cellulose the alternating

orientation of β-glucose results in a straight chain. This allows formation of

bundles of molecules arranged in parallel. Hydroxyl groups are regularly spaced

along each cellulose molecule, allowing many hydrogen bonds to form between

the molecules. These bundles of cellulose molecules are c alled microbrils

s
and are the basis of plant cell walls. Microbrils have very high tensile strength

bec ause of the strong covalent bonds in the cellulose molecules, the number of

s
molecules and the cross-links between them. The strength prevents plant cells

e
from bursting, even when very high pressures have developed inside the cell due

to entry of water by osmosis.

r
P

y
l
y

n
▴ Figure 17 Part of a cellulose molecule viewed from the side, showing eight glucose

subunits. C arbon atoms are grey, oxygen red and hydrogen green

O
i
B1.1.7 Role of glycoproteins in cell–cell

s
recognition

y
Glycoproteins are composed of polypeptides with c arbohydrate attached.
e

p
In most c ases, the c arbohydrate is an oligosaccharide — a short chain of

monosaccharides linked by glycosidic bonds. Glycoproteins are a component

v

of plasma membranes in animal cells and are positioned with the attached

c arbohydrate facing outwards. By displaying distinctive glycoproteins, cells

o
i

allow other cells to recognize them. The glycoprotein on the surface of one cell is
n

recognized by receptors on the surface of another cell.

U

Cell-to-cell recognition helps with the organization of tissues and c an also allow
n

foreign cells or infected body cells to be identied and destroyed. The ABO

antigens in red blood cells are an example of glycoproteins providing the means

of cell–cell recognition.
o
d

ABO glycoproteins
i
r

Red blood cells have glycoproteins in their membranes Key N acetyl-galactosamine furanose
t

that do not have a known function, but that aect

o

blood transfusion. Any of three possible types of

A
oligosaccharide c an be present on the glycoprotein.
f

The oligosaccharides are c alled O, A and B. One or

x

two of these types of glycoprotein are present in every

l

person’s blood, but not all three.

O

If blood containing glycoprotein A is transfused into

a person who does not produce it themself, the

v

blood will be rejected. Similarly, blood containing

glycoprotein B is rejected if a person does not produce

E

it themself. However, glycoprotein O does not c ause

rejection problems, bec ause it has the same structure

part of the glycoprotein that projects out from the

as A and B with one monosaccharide less, so is not

plasma membrane of the red blood cell

recognized as foreign.

▴ Figure 18 O, A and B glycoproteins in red blood cells

187
 Form and function

B1.1.8 Hydrophobic properties of lipids

Lipids are a diverse group of substances in living organisms that dissolve in

non-polar solvents. Ethanol, toluene and propanone (acetone) are examples of

non-polar solvents. Lipids are only sparingly soluble in aqueous (water-based)

s
solvents. For this reason, they are said to be hydrophobic. This is a rather

misleading term, bec ause lipids are not repelled by water — they are just more

s
attracted to non-polar substances.

e
F ats, oils, waxes and steroids are classes of commonly occurring lipids.

▴ Figure 19 Fatbergs are an increasing

r
• Oils have a melting point below 20°C, so they solidify at low temperatures.

problem is sewers. Warm liquid fat from

P
• F ats have a melting point between 20°C and 37°C so they are solid at room
food waste cools and solidies in sewers

y
bec ause it does not dissolve in water. This temperature and liquid at body temperature.

sewer under the Strand in London has large

l
• Waxes have a melting point above 37°C, so they liquify at high temperatures.

fat accumulations

n
• Steroids have molecules with a characteristic four-ring structure.

O
i
B1.1.9 Formation of triglycerides and

s
phospholipids by condensation reactions

y
A triglyceride is made by combining three fatty acids with one glycerol. Each of
e

p
the fatty acids is linked to the glycerol by a condensation reaction, so three water

molecules are produced. The linkage formed between each fatty acid and the
v

glycerol is an ester bond. This type of bond is formed when an acid reacts with

o
i

the hydroxyl group (–OH) in an alcohol. In this case, the reaction is between the

carboxyl (–COOH) group on a fatty acid and a hydroxyl on the glycerol. These
n

groups are the only hydrophilic parts of fatty acid and glycerol molecules and are

used up in the condensation reaction, so triglycerides are entirely hydrophobic.

U

Depending on the type of fatty acids they contain, triglycerides may be oils orfats.
n

glycerol

fatty acids
o
d

triglyceride (fat)
H

H
i
r

HO C (CH ) CH O C (CH ) CH
2 n 3 2 n 3

H
t
o

O O
condensation
a

(water removed)
H HO C (CH ) CH O C (CH ) CH
2 n 3 2 n 3
f

O O
x

H
l

HO C (CH ) CH O C (CH ) CH
2 n 3 2 n 3
O

H
O O
H

3H O
v

Ester bond

▴ Figure 20 Formation of a triglyceride from glycerol and three fatty acids

E

188
 Molecules

Phospholipids have a structure similar to triglycerides, but there are two fatty OH

hydrophilic
acids linked to glycerol, with a phosphate group instead of a third fatty acid. The
O P O

phosphate
phosphate is hydrophilic, so phospholipid molecules are partly hydrophilic and

head
partly hydrophobic.

H C H H
H

s
C C

O O

s
H

B1.1.10 Dierence between saturated,

C O C O

e
monounsaturated and polyunsaturated
C H C H

C H H

r
fattyacids

C H H

P
F atty acids have an unbranched chain of c arbon atoms, with hydrogen atoms

y
C H C H
covalently bonded, so it is a hydroc arbon chain. The acid part of the molecule

is a c arboxyl group (–COOH) at one end of the chain. At the other end there is a C H C H

l
methyl group (–CH ). The length of the hydroc arbon chain is variable but most of

y
C H C H

n
3

the fatty acids used by living organisms have between 14 and 20 c arbon atoms.

C H C H
hydrophobic

t
hydrocarbon

O
Another variable feature of fatty acids is the covalent bonding between the C H H C H

i
tails
c arbon atoms. Some have single bonds between all the c arbon atoms, whereas
C H H H

s
others have double bonds between some pairs of c arbon atoms in the chain.

C H H

C arbon atoms linked by single bonds c an also bond to two hydrogen atoms.

r
H C H H

y
C arbon atoms linked by a double bond to an adjacent c arbon in the chain,

H C H C H
e
c an only bond to one hydrogen. A fatty acid with single bonds between all of

p
its c arbon atoms contains as much hydrogen as it possibly could and is c alled C H C H
v

a saturated fatty acid. F atty acids that have one or more double bonds are
C H C H

o
unsaturated bec ause they contain less hydrogen than they could. If there is one

C H H
i

double bond, the fatty acid is monounsaturated; if it hasmore than one double

C H C H
n

bond, it is polyunsaturated.

C H H

Nearly all unsaturated fatty acids in living organisms have the hydrogen atoms
U

H H

on the same side of the two double-bonded c arbon atoms — these are c alled
n

▴ Figure 21 The molecular structure of

cis-fatty acids. The alternative arrangement is for the hydrogens to be on opposite

a phospholipid. The phosphate oen has

sides — these are c alled trans-fatty acids. In cis-fatty acids, there is a bend in the

other hydrophilic groups attached to it, but

o
d

hydroc arbon chain at the double bond. This makes triglycerides containing

these are not shown in this diagram

cis-unsaturated fatty acids less good at packing together in regular arrays than
i

saturated fatty acids, so they have a low melting point. So, triglycerides with cis-
r

unsaturated fatty acids are usually liquid at room temperature — they are oils.
t
o

Trans-fatty acids do not have a bend in the hydroc arbon chain at the double

bond; they have straight chains and a higher melting point. They are solid at
f

room temperature. They are produced articially by partial hydrogenation of

x

vegetable or sh oils. This is done to produce solid fats for use in margarine and
l

some other processed foods, but serious health concerns have led the Food and
O

Drug Administration (FDA) in the US to ban use of industrial trans-fats.

v
E

189
 Form and function

O OH

O OH O OH

C C C

s
s
H C H C H C H

e
C C H C H

C C H C H

r
C C H C H

y
C C H C H

l
y
C C H H C H

n
C C H H C H

O
i
H C H C C H

s
H C H C H C H

y
C C H H C H
e

p
H C H C H C H
v

H C H C H H C H

o
i

C C H H C H
n

C C H C H
U

C C H C H
n

H H H
o

palmitic acid linolenic acid palmitoleic acid

d

• saturated • polyunsaturated • monounsaturated

• non-essential • all cis • cis

i
r

• essential • non-essential
t
o

• omega 3 • omega 7
a

▴ Figure 22 Examples of fatty acids. The omega number indic ates how far
f

from the methyl group the rst double bond is loc ated
u
x

l
O

a
v
E

▴ Figure 23 Sunower oil is pressed from the seeds.

▴ Figure 24 Butter is made by churning cream from cow’s milk.

Two-thirds of the fatty acids in the oil are polyunsaturated

Two-thirds of the fatty acids in butter are saturated and most of the

and most of the rest are monounsaturated

rest is monounsaturated

190
 Molecules

H H H

C C C C

cis

s
trans

s
▴ Figure 25 Double bonds in fatty acids

e
r
P

y
l
y

n
t

O
i
s
r

y
▴ Figure 26 S aturated fatty acids have straight chains. Monounsaturated fatty acids have
e

p
one kink in the chain and polyunsaturated fatty acids have more than one kink so they c an

become curved
v

o
i

ATL Research skills: Using Google Scholar for research

n

A 2017 journal article by the Americ an Heart Figure 27 on the next page shows the Google Scholar
U

Association estimated that replacing saturated fat with entries for two dierent journal articles

polyunsaturated fat in the diet has the potential to reduce

n

1. Contrast the two papers in terms of citation frequency

the risk of c ardiovascular diseases by 30%. On the other

and currency.

hand, a small number of scientists have challenged the

o
d

2. Is there a consensus view on saturated fat in the diet?

negative press received by saturated fats. Google Scholar

What challenges arise when the media reports both

is a search engine that allows a researcher to focus their

i

points of view without acknowledging which is the

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search on scholarly literature. You might use it for your

t

consensus of the scientic community?

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o

a
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u
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l
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a
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191
 Form and function

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▴ Figure 27 This annotated page gives tips on using Google Scholar for research. The two dierent entries take a dierent view on the

p
role of saturated fat in the diet
v

o
i
n

B1.1.11 Triglycerides in adipose tissues for

U

energy storage and thermal insulation

n

Triglycerides are used for energy storage in plants and animals. In animals, the

triglycerides are fats and are stored in specialized groups of cells c alled adipose
o
d

tissue. In humans, adipose tissue is loc ated immediately beneath the skin and

also around some organs including the kidneys.

i
r

The properties of triglycerides make them particularly suitable for long-term

t
o

energy storage.
a

• They are chemic ally very stable, so energy is not lost over time.
f

• They are immiscible with water, so they naturally form droplets in the
x

cytoplasm which do not have osmotic or other effects on the cell.

l

• They release twice as much energy per gram in cell respiration as

O

c arbohydrate, so enough energy c an be stored in half the body mass. This is

important for animals that move and especially for birds and bats that fly.
v

• They are poor conductors of heat, so they c an be used as a thermal insulator

in animals that need to conserve body heat.

E

• They are liquid at body temperature, so they c an act as a shock absorber — for

example, around the kidneys.

192
 Molecules

Thermal insulation is needed most by animals that live in cold habitats and that

maintain a body temperature much higher than the environment. Such animals

have thick layers of subcutaneous adipose tissue. In marine mammals it is

c alled blubber. In animals such as sea lions there are sometimes problems with

overheating when adults emerge onto land to breed, bec ause the thick layer of

s
blubber impedes dissipation of heat produced by metabolism and the air is much

s
warmer than the water in the ocean habitat.

e
▴ Figure 28 A typic al 40 kg male emperor

r
B1.1.12 Formation of phospholipid bilayers
penguin has 12.7 kg of body fat at the

start of winter, but only 2.4 kg at the end.

P
as a consequence of the hydrophobic and

y
Whydo male emperor penguins need such

hydrophilic regions a large amount of body fat at the start of

l
thewinter?

y
Substances attracted to water are c alled hydrophilic. Other substances that

n
are not attracted to water are c alled hydrophobic. Phospholipids are unusual

t
bec ause part of a phospholipid molecule is hydrophilic and part is hydrophobic.

O
Substances with this property are described as amphipathic. The hydrophilic part

i
of a phospholipid is the phosphate group. The hydrophobic part consists of the

s
two hydroc arbon chains. The chemic al structure of phospholipids is described

r
in Section B1.1.9. The structure c an be represented simply using a circle for the

y
phosphate group and two lines for the hydroc arbon chains.
e

p
v

o
i

▴ Figure 29 Simplied diagram of a phospholipid molecule

n

The two parts of the molecule are oen c alled the phosphate head and the

hydroc arbon tails. When phospholipids are mixed with water the phosphate
U

heads are attracted to the water but the hydroc arbon tails are attracted to
n

each other more than to the water. Bec ause of this the phospholipids become

arranged into double layers, with the hydrophobic hydroc arbon tails facing
o

inwards and the hydrophilic heads facing outwards to the water on either side.
d

These double layers are c alled phospholipid bilayers. They are stable structures
i

and they form the basis of all cell membranes.

r

t
o

hydrophilic phosphate head

a
f

hydrophobic hydrocarbon tails

u
x

phospholipid

bilayer
l
O

a
v
E

▴ Figure 30 Simplied diagram of a phospholipid bilayer

193
 Form and function

B1.1.13 Ability of non-polar steroids to pass

through the phospholipid bilayer

Steroids are a group of lipids with molecules similar to sterol. They c an be

identied using these features:

s
B
D

• four fused rings of c arbon atoms

s
A C • three cyclohexane rings (Figure 31; A, B and C) and one cyclopentane ring

e
(Figure 31; D)

• 17 c arbon atoms in total in the rings.

r
▴ Figure 31 The four-ring structure

ofsteroids

P
There are hundreds of examples of steroids, which dier in the position of C=C

y
double bonds and in the functional groups such as –OH that are added to the

four-ring structure. Steroids are mostly hydroc arbon and therefore hydrophobic.

l
This allows them to pass through phospholipid bilayers and enter or leave cells.

n
OH OH

t
CH CH
3 3
▸ Figure 32 Testosterone and

O
i
oestradiol have very similar molecular

structures despite their markedly

s
CH
3

dierent eects on the body. In these

r
skeletal diagrams, the c arbon atoms are

y
not individually shown but the bonds
e
between them are. Hydrogen atoms

p
attached to the c arbon are not shown

O
HO
v

but c an be inferred bec ause each

testosterone oestradiol

o
c arbon atom has a total of fourbonds
i
n

Linking questions
U

1. How c an compounds synthesized by living organisms accumulate and

n

become c arbon sinks?

a. Describe the relationship between the process of ecologic al

o
d

succession and changes in biomass. (D4.2.13)

b. Outline the events of the C alvin cycle. (C1.3.17)

i
r

c. O utline four sinks from which c arbon is being released due to human
o

activity. (C4.2.19)
a

2. What are the roles of oxidation and reduction in biologic alsystems?

f

u
x

a. Outline the role of oxidation in the release of energy from

c arbohydrates. (B1.1.4)
l
O

b. Explain the role of NADP in photosystem 1 and the C alvin cycle.

a

(C1.3.13)
v

c. O utline one example of chemoautotrophy. (C4.2.7)

E

194
B1.2 Proteins

What is the relationship between amino acid sequence and the diversity in form and function

s
ofproteins?

s
Every protein contains one or more polypeptides. The 20 dierent amino acids that c an be used to assemble

e
polypeptides are chemic ally diverse. There are parallels with the linking of letters of the alphabet to form words:

any length and sequence is possible, but only a small proportion of the possibilities are used. A dierence is that

r
polypeptides are much longer than words—most have hundreds or even thousands of amino acids. How does the

sequence of amino acids in polypeptides determine their three-dimensional shape? How is the shape of a protein

y
relatedto its function?

l
y

n
How are protein molecules aected by their chemic al and physic al environments?

O
Relatively weak interactions within protein molecules

i
maintain the conformation needed for functions to be

s
performed. These interactions are sensitive to the physic al

r
and chemic al environment. How do changes of pH

y
c ause protein structure to be altered? How do heavy
e
metals such as mercury c ause misfolding of proteins?

p
How does heat aect the structure of proteins? Why do
v

some environmental changes lead to denaturation? What

are some examples of proteins that function in extreme

o
i

environments such as high or low temperatures? Low or

n

high values of pH?

U

n
o
d

▴ Figure 1 Some protein structures

i
r

SL and HL AHL only

o

B1.2.1 Generalized structure of an amino acid B1.2.6 Chemic al diversity in the R-groups of amino acids

B1.2.2 Condensation reactions forming dipeptides and as a basis for the immense diversity in protein form and
f

longer chains of amino acids function

x

B1.2.3 Dietary requirements for amino acids B1.2.7 Impact of primary structure on the conformation

B1.2.4 Innite variety of possible peptide chains ofproteins

l
O

B1.2.5 Eect of pH and temperature on protein structure B1.2.8 Pleating and coiling of secondary structure of
a

proteins

B1.2.9 Dependence of tertiary structure on hydrogen

v

bonds, ionic bonds, disulde covalent bonds and

hydrophobic interactions
E

B1.2.10 Eect of polar and non-polar amino acids on tertiary

structure of proteins

B1.2.11 Q uaternary structure of non-conjugated and

conjugated proteins

B1.2.12 Relationship of form and function in globular and

brous proteins

195
 Form and function

B1.2.1 Generalized structure of an amino acid

Amino acids are the building blocks of proteins. E ach amino acid molecule has a

central c arbon atom c alled the alpha c arbon, with single covalent bonds to four

other atoms. One of these is the nitrogen atom of an amine group and another

s
is the c arbon atom of a c arboxyl group. The c arboxyl group (–COOH) is acidic

bec ause it c an donate a proton and the amine group is basic bec ause it c an

s
accept one, so amino acids are amphiprotic.

e
The alpha c arbon atom also has a single covalent bond to a hydrogen atom. The

r
other covalent bond links the alpha c arbon to a side chain, c alled the R-group.

The R-group c an be any one of a wide range of possibilities.

y
▸ Figure 2 The generalized structure of an H
O O
H H

amino acid c an be represented in dierent

l
ways. Which of these is most informative?
H N C COOH
N C C H O

y
2 N C H

n
H
C O

R
R

t
H

O
i
s
Activity: Researching B1.2.2 Condensation reactions forming

y
residues dipeptides and longer chains of amino acids
e

p
To form a dipeptide, two amino acids are linked by a condensation reaction.

The R in “R-group” stands for

v

More amino acids c an be linked by further condensation reactions to create

residue.

o
a longer chain. Polypeptides c an contain any number of amino acids, though
i

1. What is a residue?

chains of fewer than 20 amino acids are usually referred to as oligopeptides

n

2. When does the R-group rather than polypeptides. Polypeptides are the main component of proteins.

become a residue?

Amino acids are linked with peptide bonds. These are C N bonds formed by
U

a condensation reaction between the amine group ( NH ) of one amino acid

2
n

and the c arboxyl group ( COOH) of another. The reaction is c atalysed in cells

by ribosomes. It is a directional process: the amine group of a free amino acid is

o
d

linked to the c arboxyl group at the end of the growing chain. Bec ause peptide

bonds are made using groups that are part of all amino acids, the bond is the
i
r

same, whatever the R-groups of the amino acids are.

t
o

peptide bond
a

carboxyl amino
f

group group
u

H H H O H H
condensation
x

O O
O
H H H
(water removed)
l

+
O

N C C N C C N C C N C C
a

H OH H H OH
OH
v

R R R R
E

H O
2

▴ Figure 3 Condensation joins two aminoacids with a peptide bond to produce

adipeptide

196
 Molecules

Activity: Drawing dipeptides and oligopeptides

To test your skill at showing how peptide bonds are formed, try showing the formation of a peptide bond between two

of the amino acids in Figure 4. There are 16 possible dipeptides that c an be produced from these four amino acids.

s
COOH

s
OH
H C H H

e
H C H
H C H H C H H

H N C COOH
2 H N C COOH H N C COOH H N C COOH

r
2 2 2

H
H H H

y
serine glutamic acid alanine glycine

l
▴ Figure 4 Some common amino acids

n
You could also draw an oligopeptide of four amino acids, linked by three peptide bonds. If you do this correctly, you

t
should see the following features.

O
• A chain of atoms linked by single covalent bonds forming the backbone of the oligopeptide, with a repeating sequence

i
C→ N→ C
→

→
of N C C . If this is shown as a zigzag (N C C ) the bond angles are closer to being correct.

s
• A hydrogen atom is linked by a single bond to each nitrogen atom in the backbone and an oxygen atom is linked by

y
a double bond to one of the two c arbonatoms. e
• The amine ( NH ) and c arboxyl ( COOH) groups are used up in forming the peptide bond and only remain at the

p
2

ends of the chain. These are c alled the amino and c arboxyl terminals.
v

• The R-groups of each amino acid remain and project outwards from the backbone.

o
i
n

Computer modelling
U

Atom and Bond Edit So Hel Slide ◂ Figure 5 This image of the dipeptide
n

glycine-alanine was constructed using the

H B C Si

web-based computer applic ation c alled

N P O S
o

ChemM agic from the University of Illinois.

d

F Cl Xx inv
Similar molecule builder apps exist on

Q – otherwebsites
Q + redo undo
i
r

Single Double rile

o

The app begins with a molecule of

a

Xatm Xbnd Xmol

methane. Students then substitute

individual atoms with desired atoms.

f

ire Ball Sae

u

 1. Using Figure 5, deduce what



 
x

colours represent oxygen, c arbon,

oad odel
l

nitrogen and hydrogen.

O

Name Dra
a

2. Identify the R-groups of glycine

Ceagi File

and alanine.
v

Oter odel Ation

Carge Diole
E

B1.2.3 Dietary requirements for amino acids

Twenty dierent amino acids are used by ribosomes to make polypeptides.

Plants c an make all of these by photosynthesis. Animals obtain amino acids from

their food. An essential amino acid is one that c annot be synthesized in sucient

quantities by the animal so must be obtained from the diet. A non-essential amino

197
 Form and function

acid c an be synthesized by an animal using metabolic pathways that transform

one amino acid into another.

Nine of the 20 amino acids are essential in humans. The others are non-essential,

though several become essential in special circumstances. For example, the amino

s
acid phenylalanine is essential because it cannot be synthesized by the human body;

tyrosine is non-essential because it can be made from phenylalanine.

s
e
COOH COOH

phenylalanine hydroxylase

+ O

r
NH NH
2 2

HO

y
phenylalanine tyrosine

▴ Figure 6 Conversion of an essential amino acid into a non-essential amino acid

l
y

n
Foods vary in their amino acid content. It is possible to eat a protein-rich diet and

still be decient in an essential amino acid. Animal-based foods (sh, meat, milk,

O
eggs) have a balance of amino acids that is similar to what is needed in the human

i
diet. Plant-based foods have a dierent balance and some are decient in specic

s
amino acids. For example, cereals such as wheat have a low lysine content, and

peas and beans are low in methionine. Both lysine and methionine are essential

y
amino acids for humans. So, people eating a vegan diet, must ensure that
e
enough of each essential amino acid is consumed. Traditional plant-based diets

p
in successful civilizations do provide such a balance.
v

o
Data-based questions: Essential amino acids
i
n

1. Table 1 summarizes the relative content of essential a. Outline what is meant by the term “essential

amino acids in dierent foods. Cysteine and tyrosine amino acid”. [2]

are classied as being “conditionally essential”.

U

b. Evaluate human milk as an overall source of

Thequantity of each amino acid in a hen egg is set

essential amino acids. [2]
n

as 1.0 and all other values are relative to the hen

c. Phenylalanine is converted to tyrosine by the

eggstandard.
enzyme phenylalanine hydroxylase.
o
d

Deduce the reason that tyrosine is considered

hen’s human cow’s

aconditionally essential amino acid. [1]

i

eggs milk milk

r

d. When infants with the condition phenylketonuria

t

isoleucine 1.0 1.1 1.1

o

(PKU) are le untreated, they have a build-up of

a

leucine 1.0 1.4 1.3

phenylalaninein their blood and high levels of
f

valine 1.0 1.0 1.0 phenylalanine in their urine. Suggest the c ause
u

of this condition. [1]

x

threonine 1.0 1.0 0.9

l

methionine
O

1.0 1.1 0.7

and cysteine
a

tryptophan 1.0 1.6 1.3

v

lysine 1.0 1.0 1.3

E

phenylalanine

1.0 1.0 0.9

and tyrosine

histidine 1.0 0.9 1.1

◂ Table 1

[Source: D ata obtained from Robert McGlivery,

Biochemistry: A Functional Approach, 1970, W. B.

S aunders.]

198
 Molecules

B1.2.4 Innite variety of possible

Activity: F amous

peptidechains
vegetarians and

Ribosomes link amino acids together one at a time, until a polypeptide is fully
vegans

s
formed. The ribosome c an make peptide bonds between any pair of amino

acids, so all sequences are possible. Ribosomes do not make random sequences

s
of amino acids. They receive instructions in the form of genetic code. Twenty

dierent amino acids are included in the code.

e
The number of possible amino acid sequences c an be c alculated starting with

r
dipeptides. Both amino acids in a dipeptide c an be any of the 20, so there are

P
20 × 20 possible sequences (20 ). There are 20 × 20 × 20 possible tripeptide

y
3 n

sequences (20 ). For a polypeptide of n amino acids, there are 20 possible

sequences. The number of amino acids in a polypeptide c an be anything from 20

l
y
to tens of thousands.

n
400

For example, if a polypeptide has 400 amino acids, there are 20 possible

t
▴ Figure 7 Leonardo da Vinci is

O
amino acid sequences. This is an incredibly large number, and some online

i
reported to have said that he did

c alculators simply express it as innity. Given that the number of amino acids

s
not want his body to be a tomb for

in a polypeptide c an be tens of thousands, the number of possible sequences

other creatures and was probably

is eectively innite. But only an extremely small proportion are made by an

r
vegetarian. C anyou nd other examples

y
organism. This is the organism’s proteome.

of great thinkers who bec ame vegan

e
orvegetarian?

p
Examples of polypeptides
v

• Beta-endorphin is natural pain killer secreted by the pituitary gland that is a

o
polypeptide of 31 amino acids.
i

• Insulin is a small protein that contains two short polypeptides, one with 21
n

amino acids and the other with 30.

• Alpha amylase is the enzyme in saliva that starts the digestion of starch. Itis a
U

single polypeptide of 496 amino acids, with one chloride ion and
n

one c alcium ion associated.

• Titin is the largest polypeptide discovered so far. It is part of thestructure of

o
d

muscle. In humans, titin is a polypeptide of 34,350 amino acids, but in mice

it is even longer with 35,213amino acids.

i
r

t
o

B1.2.5 Eect of pH and temperature on

f

▴ Figure 8 This image of insulin c an be

u

protein structure viewed and rotated on the PDB Molecule of

x

the Month website

The three-dimensional conformation of proteins is stabilized by bonds or

l
O

interactions between the R-groups of amino acids within the molecule. Most of
a

these bonds and interactions are relatively weak and they c an be disrupted or

broken. This results in a change to the conformation of the protein and is c alled
v

denaturation.
E

A denatured protein does not normally return to its former structure — the

denaturation is permanent. Soluble proteins oen become insoluble and form a

precipitate. This is due to the hydrophobic R-groups in the centre of the molecule

becoming exposed to water by the change in conformation.

199
 Form and function

Heat c an c ause denaturation bec ause it c auses vibrations within the molecule

that c an break intermolecular bonds or interactions. Proteins vary in their heat

tolerance. Some microorganisms that live in volc anic springs or in hot water near

geothermal vents have proteins that are not denatured by temperatures of 80°C

or higher. The best-known example is DNA polymerase from Thermus aquaticus,

s
a prokaryote that was discovered in hot springs in Yellowstone National Park.

It works best at 80°C and bec ause of this it is widely used in biotechnology.

s
Nevertheless, heat c auses denaturation of most proteins at much lower

e
temperatures.

r
Extremes of pH, both acidic and alkaline, c an c ause denaturation. This is

bec ause positive and negative charges on R-groups are changed, bre aking

y
ionic bonds within the protein or c ausing new ionic bonds to form. As with
▴ Figure 9 When eggs are heated,

proteins that were dissolved in both he at, the three-dimensional structure of the protein is altered and proteins that

l
the white and the yolk are denatured. have been dissolved in water oen become insoluble. There are exceptions:

n
They become insoluble so both yolk and
the contents of the stomach are normally acidic, with a pH as low as 1.5, but

whitesolidify
this is the optimum pH for the protein-digesting enzyme pepsin that works

t
inthe stomach.

O
i
s
r
Applying techniques: Using a colorimeter to measure turbidity:

y
denaturation experiments
e

p
v

A colorimeter and a spectrophotometer are both

o
instruments that measure the amount of light that passes
i

through a sample. If a colorimeter is set at 500 nm or

as close to the UV range as possible it means that it will

n

emit blue light into the sample. If there is a function

choice, choose transmittance to measure how much light

U

has passed through the sample. If the function is set at

n

absorbance, the machine will measure how much light

has been absorbed.

o
d

Albumen is one of the main proteins in egg white. A

solution of egg albumen in a test tube c an be heated in a

i
r

water bath to nd the temperature at which it denatures.

t

The eects of pH c an be investigated by adding acids and

o

alkalis to test tubes of egg albumen solution. ▴ Figure 10 These tubes contain increasing quantities of
a

denatured albumin. The concentration of albumin in urine is an

To quantify the extent of denaturation, a colorimeter
f

important diagnostic for determining kidney function. Albumin

u

c an be used, as denatured albumen absorbs more

x

in urine is precipitated using sulphosalicylic acid, which results

light than dissolved albumen. The solution will become

in turbidity. This c an be measured using a colorimeter. Protein

moreturbid.
l

should not normally be present in urine

O

a
v
E

200
 Molecules

LHA
Elements in Number of
B1.2.6 Chemic al diversity in the R-groups

R-group amino acids

of amino acids as a basis for the immense

H only 1

diversity in protein form and function

C and H only 5

s
The 20 amino acids that ribosomes use to make polypeptides are very varied in
C, H and S only 2

the chemic al nature of their R-groups. The elements present in the R-groups are

s
C, H and N only 5

shown in Table 2.

e
C, H and O only 5

When amino acids are linked up into a polypeptide, their amine and c arboxyl
C, H, N and O 2

r
groups are used to make peptide bonds. This leaves an amine group (–NH )
2

▴ Table 2 Variation in R-groups of

at one end of the chain and a c arboxyl group (–COOH) at the other end. The

y
aminoacids
hydrogen atom attached to the alpha c arbon atom of each amino acid has little

eect on the properties of the polypeptide; it is the R-groups that determine

l
the chemic al characteristics. Some of the R-groups are hydrophobic and some

n
hydrophilic. Of the hydrophilic R-groups, some are polar and others become

charged (+ or −) by acting as an acid or a base. This broad diversity of R-groups

t
allows living organisms to make and use an amazingly wide range of proteins.

O
i
Some of the dierences between R-groups are shown in Table 3.

s
Nine R-groups are hydrophobic Eleven R-groups are hydrophilic

y
with between zero and nine
e
Seven R-groups can become charged

carbon atoms Four

p
hydrophilic
v

Four R-groups act as Three R-groups act as

Three R-groups are

o
Six R-groups

an acid by giving up a a base by accepting a

i

R-groups do not contain polar but never

proton and becoming proton and becoming

n

contain rings rings charged

negatively charged positively charged

U

▴ Table 3 Classic ation of amino acids

n

Some proteins contain amino acids that are not in the basic repertoire of 20.

In most c ases this is due to one of the 20 being modied aer a polypeptide
o
d

has been synthesized. There is an example of modic ation of amino acids

in collagen, a structural protein used to provide tensile strength in tendons,

i
r

ligaments, skin and blood vessel walls. Collagen polypeptides made by

t

ribosomes contain proline at many positions, but at some of these positions it is

o

converted to hydroxyproline, which makes the collagen more stable.

a
f

u
x

B1.2.7 Impact of primary structure on the

l
O

conformation of proteins
a

The structure of proteins has four levels of complexity: primary, secondary, tertiary
v

and quaternary. Primary structure is the linear sequence of amino acids in a

polypeptide.
E

The backbone of a polypeptide is a repeating sequence of atoms linked

by covalent bonds ( C C N C C N and so on). The bond angles are all

tetrahedral and there c an be rotation about the bonds between the alpha c arbon

atoms and adjacent nitrogen and c arbon atoms. This allows polypeptides to fold

into almost any three-dimensional shape.

201
 Form and function
LHA

▸ Figure 11 Rotation about bonds

H

O
R
in a polypeptide

C-α

s
N-terminus
C

C-α

s
N
C

e
C-α
C-terminus

r
O

peptide bond

y
(no rotation)

rotation about

l
carbon bonds

n
The three-dimensional arrangement of atoms in a polypeptide or protein

t
is its conformation. Most polypeptides self-assemble into a specic

O
i
conformation determined by the sequence of amino acids and their R-groups.

s
The conformation of proteins determines their functions and through this

the behaviour of cells. This is why protein conformation is of great interest

y
tobiologists. e
Since the 1970s, biologists have used experimental procedures to determine

p
the structures of more than 180,000 proteins. These have been deposited in the
v

Protein D ata Bank, a freely available online resource. This is only a small fraction

of the naturally occurring proteins. To speed

o up the working out of protein
i

conformations, articial intelligence and massive computing power is being used

n

to make predictions based on primary structure. This will, for example, allow all

protein conformations in the human proteome to be discovered relatively quickly.

U

B1.2.8 Pleating and coiling of secondary

o
d

structure of proteins
i
r

At regular intervals along a polypeptide chain there are C=O and N H groups.
t

They are what remains of c arboxyl and amine groups aer they have been
o

used to make peptide bonds. Both C =O and N H are polar, with the oxygen

having a slight negative charge and the hydrogen a slight positive charge. Due
f

to this polarity, hydrogen bonds c an form between these groups. Although

x

hydrogen bonds are individually weak, the frequency of C=O and N H groups

along polypeptide chains allows many of them to form and collectively they
l
O

are strong enough to stabilize distinctive conformational structures within

a

proteinmolecules.
v

Two commonly occurring types of structure are stabilized by hydrogen bonding.

• The α-helix — the polypeptide is wound into a helic al shape, with hydrogen
E

bonds between adjacent turns of the helix.

• The β-pleated sheet — two or more sections of polypeptide are arranged in

parallel with hydrogen bonds between them. The sections of polypeptide

run in opposite directions, forming a sheet that is pleated bec ause of the

tetrahedral bond angles.

202
 Molecules

LHA
Regular structures stabilized by hydrogen bonding within polypeptides are the

secondary structure of a protein.

alpha helix

s
N H
beta-pleated sheet
C
C
O

s
N H
O
H O
H O
O

C
C C N
C
C N
C

e
H C C C
N C N
N C
H C N C
C N
C
C

C
H H
N O
N H
C O H
O O

r
C
▴ Figure 12 Beta barrel proteins in
hydrogen

O
H
O membranes have large β-pleated sheets

P
bond H O
H

y
C O H
O
C
H C
N curved to form a cylinder. What functions
C C C
N
C N C
N C N N
C
C N C C
O c an they perform?
C
O
N C

l
C
O
O
H H O
H
O

y
C

n
H H
C

t
C
N N
C
O

O
i
O

s
r
▴ Figure 13 The α-helix (le) and the β-pleated sheet (right) are examples of

y
secondarystructures
e

p
B1.2.9 Dependence of tertiary structure
v

on hydrogen bonds, ionic bonds, disulde

o
i

covalent bonds and hydrophobic interactions

n

Tertiary structure is the folding of a whole polypeptide

U

hydrophobic
chain into a three-dimensional structure. This structure

interaction
n

is stabilized by interactions between R-groups. There

CH

are four main types of interaction.

H C CH
3 3 polypeptide
CH
o

2
• Ionic bonds between positively charged and
d

H C CH
3 3 backbone

negatively charged R-groups. Amine groups

O

CH
i

become positively charged by accepting a proton H

r

hydrogen
+ +
2 3

( NH + H → –NH ). C arboxyl groups become

t

bond O
o

positively charged by donating a proton ( COOH

a

→ –COO + H ). Bec ause of the involvement of OH

C
f

CH S
protons (hydrogen ions), ionic bonds in proteins
2 2
u

CH
2
are sensitive to pH changes.
x

disulfide bridge

• Hydrogen bonds between polar R-groups.

l
O

A hydrogen atom forms a link between two

a

electronegative atoms such as O or N. It is

O

covalently bonded to one of them, which results

v

CH CH CH CH NH O
3
in the hydrogen having a slight positive charge, 2 2 2 2 2

making it attractive to the other, which has a slight ionic bond

E

negative charge.

• Disulfide bonds between pairs of cysteines. This

is a covalent bond and the strongest of all the

interactions.

▴ Figure 14 R-group interactions contribute to tertiary structure

• Hydrophobic interactions between any of the

non-polar R-groups.

203
 Form and function
LHA

Tertiary structure develops as a polypeptide is synthesized by the ribosome. In

some c ases, a chaperone protein helps with this process to ensure that it results

in a correctly folded and fully functional protein.

A wide range of three-dimensional shapes is produced, most of which are

s
globular. Within these tertiary structures there are oen parts with secondary

structure — α-helices and/or β-pleated sheets.

s
Some polypeptides do not become folded and instead remain elongated — they

e
do not have tertiary structure. These are brous proteins and have structural roles,

which are described in Section B1.2.12

r
P

y
B1.2.10 Eect of polar and non-polar amino

l
y
acids on tertiary structure of proteins

n
Amino acids in proteins c an be divided into two broad c ategories:

O
• non-polar and therefore hydrophobic

i
• polar or charged and therefore hydrophilic.

s
r
M any globular proteins need to be soluble in water bec ause they c arry out

y
their function in the cytoplasm or in an aqueous solution outside the cell. These
e
proteins have hydrophilic amino acids on their surface where they are in contact

p
with water and hydrophobic amino acids clustered in the centre where water is
v

excluded. This arrangement stabilizes the tertiary structure of the protein bec ause

it maximizes hydrophobic interactions

o
between amino acids in the centre and
i

hydrogen bonding between amino acids on the surface and the water around
n

the protein.
U

Some proteins are routinely in contact with non-polar substances over some or

all their surface. Such proteins have hydrophobic amino acids on parts of their
n

surface. Integral proteins embedded in membranes have hydrophobic amino

acids where they contact the non-polar hydroc arbon core of the membrane.
o
d

In transmembrane proteins this hydrophobic region is a belt, with hydrophilic

regions inside and outside that are in contact with aqueous solutions inside and
i
r

outside the cell. This arrangement both stabilizes the tertiary structure of the
t

protein and ensures that it remains positioned correctly in the membrane where
▴
o

Figure 15 Integrin is a transmembrane

a

its function c an be performed.

protein composed of two polypeptides

(shown green and blue), each with

f

Channel proteins in membranes allow hydrophilic solutes or water to diuse

u

an alpha helix of hydrophobic amino

x

across the hydrophobic core of the membrane. They have hydrophilic regions
acids embedded in the core of the

with a hydrophobic region between, which holds them in a transmembrane

membrane(grey). Integrin connects the
l
O

position. In addition, they have a tunnel lined with hydrophilic amino acids
cytoskeleton inside the cell to components
a

of the extracellular matrix, so helps bind the through the centre of the protein. The width and charge distribution of this

cells of a tissue channel allows specic hydrophilic ions or molecules to pass through.
v
E

204
 Molecules

LHA
B1.2.11 Quaternary structure of

non-conjugated and conjugated proteins

All proteins have at least one polypeptide, but many consist of two or more

polypeptides linked together and some have one or more non-polypeptide

s
components. In proteins that consist of more than a single polypeptide, the

s
three-dimensional arrangement of subunits is the quaternarystructure. beta chain beta chain

e
In a non-conjugated protein, there are only polypeptide subunits. To form

the quaternary structure the polypeptides are linked by the same types of

r
interaction as in tertiary structure. For example, insulin has two polypeptides,

P
linked by disulde bonds (shown in Figure 8 on page199). Collagen is

y
another non-conjugated protein. It consists of three polypeptides wound

together to form a rope-like structure with high tensile strength. It is

l
y
illustrated in Figure 19 on page207.

n
Conjugated proteins have one or more non-polypeptide subunits in

O
addition to their polypeptides. For example, the haemoglobin molecule

i
consists of four polypeptide chains, each associated with a haem group.

s
alpha chain haem alpha chain
The inclusion of non-polypeptide components increases the chemic al

and functional diversity of proteins. The haem group of haemoglobin

▴

r
Figure 16 The quaternary structure

y
binds oxygen, allowing this protein to transport oxygen. M any enzymes
of haemoglobin in adults consists of four
e
have a non-polypeptide component that contributes to the c atalytic
polypeptide chains (two α-chains and two

p
activity of their active site. β-chains) each of which is bound to an
v

iron-containing haem group

o
i

Data-based questions: Haemoglobin subunits during development

n

During the process of development from

Key
U

conception through to six months aer birth, human

beta-globin
alpha-globin delta-globin
n

haemoglobin changes in composition. Adult

epsilon-globin zeta-globin
gamma-globin

haemoglobin is a protein composed of two subunits

c alled globins. It has two alpha and two beta globin

o
d

subunits. Four other polypeptides are found during

development in dierent amounts: zeta, delta, 50

i
r

epsilon and gamma globins. Figure 17 illustrates

t

nibolgomeah
o

the changes in haemoglobin composition during

40
a

gestation and aer birth in a human.

f

30
1. State which two subunits are present in
u
x

thehighest amounts early in gestation. [1]

%

20
l

2. Distinguish between the changes in

O

theamountof the gamma globin with

10

theamount ofbeta globin. [2]

v

3. Determine the composition of the

0

haemoglobinat10 weeks of gestation and 10 20 30 40 2 4 6

E

weeks of gestation birth month of age

at 6 months of age. [2]

▴ Figure 17
4. State the source of oxygen for the foetus. [1]

5. Suggest reasons for the dierences in subunit

composition during foetal development and

aer birth. [3]

205
 Form and function
LHA

Experiments: Cryo-electron microscopy

A haemoglobin molecule has a diameter of about In addition to determining the form of proteins, cryo-EM

5nm. This is far too small for a light microscope to enables function to be investigated. The freezing technique

s
produce an image. Even the images produced by allows conformation changes to be revealed as a protein

electron microscopes of this size of molecule were until carries out its task.

s
recently fuzzy blobs. Improvements in technology have

e
revolutionized imaging of protein structures,

so tertiary and quaternary structures c an now

r
be determined and interactions between

proteins and other molecules. As so oen with

y
improvements in technology, this has led to a

wave of discoveries from research labs around

l
the world.

n
The new technique is cryo-electron microscopy

t
(cryo-EM). It avoids the need to crystallize

O
proteins, which is almost impossible in many

i
c ases, especially with integral membrane

s
proteins. A protein sample is applied to a

r
sample grid and is plunged into liquid ethane

y
to ash-freeze it. The protein molecules are
e
trapped in a thin layer of ice and images c an

p
then be obtained using a beam of electrons.
v

Soware has been developed for processing

the images to increase the resolution. At the

▴ o
i

Figure 18 Part of an image of the protein apoferritin generated by cryo-

start of the 21st century, the highest resolution

electron microscopy
n

possible was about 1 nanometre. By 2020,

cryo-EM had reduced this to 0.12 nm. This resolution

U

allows the position of individual atoms in a protein to be

n

discovered.
o
d

B1.2.12 Relationship of form and function in

i
r

globular and brous proteins

t
o

The function of a protein depends on its form. This c an be illustrated by

a

considering the dierence between brous and globular proteins. Fibrous

f

proteins consist of elongated polypeptides that lack the folding of typic al tertiary
x

structure. Also, the polypeptides in brous proteins do not develop secondary

structures such as alpha helices. Their quaternary structure is developed

l
O

by linking together polypeptide chains into narrow bres or laments, with

a

hydrogen bonds between the chains.

v

Collagen is an example of a brous protein. The quaternary structure is three

polypeptides, wound together into a triple helix. The primary structure of the
E

polypeptides is a repeating sequence of three amino acids: P G X. The P in

this sequence is proline or hydroxyproline, which has the special property

of preventing formation of an α-helix. The winding together of the three

polypeptides would be impossible if they were α-helices. The R-group of

every third amino acid faces inwards towards the centre of the triple helix and

glycine is the only amino acid with an R-group small enough to t: it is a single

hydrogenatom.

206
 Molecules

LHA
◂ Figure 19 Collagen—the quaternary

structure consists of three polypeptides

wound together to form a tough, rope-like

protein

s
The rope-like structure of collagen gives it very

s
high tensile strength. The R-group of amino acid

X faces outwards and is variable, allowing many

e
variations of collagen to be produced for use in

skin, tendons, ligaments, c artilage, basement

r
membranes of epithelia and the tough outer coat of

P
the eye (visible at the front as the white of the eye).

y
Globular proteins have a rounded shape, formed

l
by the folding up of polypeptides. The shape is

n
very intric ate and is stabilized by bonds between

the R-groups of the amino acids that have been

O
brought together by the folding. There are many

i
examples of the precise position of each atom in

s
a globular protein, known as the conformation,

being critic al to the protein’s function. The

y
active site of enzymes and the ligand-binding
e
site of receptors show this relationship. Insulin is

p
▴ Figure 20 The insulin receptor (blue) is an integral protein that is

another example. Only an insulin molecule has

positioned in the plasma membrane of many body cells. It has a binding site
v

the conformation needed to bind to a specic site

for insulin. When insulin binds to the receptor (right) there is a conformational

on the insulin receptor. This allows a specic and

change in the receptor, which

o conveys a signal to the interior of thecell

i

unambiguous signal to be sent to body cells when

n

blood sugar concentration is too high.

U

Linking questions

1. How do abiotic factors inuence the form of molecules?

o
d

a. Explain the eect of temperature on enzyme activity. (C1.1.8)

i
r

b. Explain why changes in pH aect the tertiary structure of proteins.

t

(B1.2.9)
o

c. O utline the relationship between light and phytohormone activity.

f

(C3.1.19)
u
x

2. What is the relationship between the genome and the proteome of

an organism?
l
O

a. Explain the mechanisms behind the regulation of transcription.

(D2.2.2)
v

b. Outline the process of translation. (D1.2.5)

E

c. Explain how a mutation in the genome c an lead to a change in the

structure of the resulting polypeptide. (D1.2.11)

207
 Form and function

TOK

What constraints are there on the pursuit

s
s
of knowledge?

e
Prematurely born infants oen have poorly developed The gold standard of investigation of the metabolic fates of

digestive tracts and must be fed nutrients through their elements is oen through use of radioisotopes or samples

r
blood vessels. This is known as total parenteral nutrition enriched in a particular rare stable isotope. Legitimately,

y
(TPN). For the infant’s skeleton to grow at the same rate parents might nd mention of such investigations worrisome.

that it would have grown in utero, very large quantities of

For this reason, most human trials must be preceded by

l
c alcium need to be dissolved in the TPN solution. Dierent

y
animal trials. For example, it has been argued that a piglet

n
c alcium salts dissolve to dierent concentrations, some

that is removed from its mother before it is weaned is a

higher than others. The question is, are all these c alcium

t
good model for prematurely born infants.

salts equally bioavailable? Does all the c alcium from a highly

O
i
soluble salt end up in the bones of the infant? How c an this

be determined? Investigating this question is a challenge

s
bec ause there are constraints on the types of investigation

y
that c an be c arried out.
e

p
v

o
i
n

C
U

▴ Figure 2 A couple consults with a medic al professional.

Sucha consultation would normally occur in human trials of

o

medic al interventions
d

There are also restrictions placed on the use of animals in

i
r

research. Ethics boards of research institutions oen have

t

▴ Figure 1 The premature baby in an incubator is receiving

o

guidelines that include:

nutrition through his blood vessels

a

• providing the justic ation for using animals

f

Parents of unwell infants may be under nancial stress

u

• reducing the total number of individuals used

and participation in compensated research might seem

x

• evidence that the experiment is not a duplic ation of

attractive. They might feel beholden to medic al experts
l

previous research
or hopeful that the novel treatment might be superior to
O

currently available treatments. Importantly, investigations • restrictions on the types of species that c an be chosen

involving human subjects are governed by research ethics

• providing details on the regimens used to eliminate or
v

committees that ensure patient’s rights are protected.

minimize pain.

Informed consent procedures require transparent

E

disclosure to subjects or their guardians of:

• the purposes of the experiment

• the limits on the ways in which their samples c an

beinvestigated.

208
 Molecules

End of chapter questions

1. Migrating birds must refuel along the way to continue 3. O utline the specific functions of three named

flying. A field study was conducted among four different proteins. [3]

s
species of migrating birds known to stop at high-quality

4. Cellulose is the most abundant organic polymer on

s
and low-quality food sites. Birds were c aptured and

E arth. Describe the structure of cellulose. [3]

blood samples were taken at the two sites.

e
5. Compare and contrast cis-fatty acids and trans-fatty

Among birds, high triglyceride concentration in blood

acids. [2]

r
plasma indic ates fat deposition whereas high butyrate

6. Proteins such as keratin and myosin consist of two or

concentration in blood plasma indic ates fat utilization

y
more alpha helices winding around each other into
and fasting.

a super-coil and are known as long coiled-coil (LCC)

The following data summarizes triglyceride levels and

l
proteins. Such proteins are involved in a wide variety of

butyrate levels measured for the same groups of birds.

y
structural and mechanic al processes in cells.

n
stinu yrartibra/noitartnecnoc

triglyceride levels butyrate levels

A study was c arried out to compare the presence of

1.8 1.4

O
1.6 LCC proteins in species from different kingdoms. The
1.2

i
1.4 LCC proteins were grouped by similarities in primary

1.0

s
1.2
structure. They were then analysed to show family

0.8
1.0
relationships and homology.

y
0.8
0.6

The diagram below shows the distribution of groups of

0.6
e
0.4

LCC protein sequences by kingdom.

p
0.4

0.2
0.2
v

animals plants

0.0 0.0

HT WS A W HT WS A W
o
i

304 47 82

species species
n

ey

HT Herit trus A Aerican robin 1 5 4

U

WS Witetroated sparro W agnolia arbler Source: A Rose,

n

S Schraegle, E

Stahlberg and
Source: Guglielmo, C.G., Cerasale, D.J. and Eldermire, C. (2005)

17
I Meier, BMC
Physiologic al and Biochemic al Zoology, 78(1), pp. 116–125. https://doi.

Evolutionary
o
d

org/10.1086/425198.

Biology, (2005),

a. Butyrate is a fatty acid. Distinguish between fatty 5, p6

prokaryotes
i
r

acids and triglycerides. [2]

a. State what determines the primary structure

t
o

b. Describe, using the triglyceride levels graph, the

of a protein. [1]
a

results at Site1 and Site2 for all the birds. [2]

b. Outline the concept of secondary structure

f

c. Explain the differences in the triglyceride level and

of proteins. [2]
u
x

butyrate level for the hermit thrush at Site1 and

c. State how many groups of LCC proteins are

Site2. [2]
l

common to all the species studied. [1]

O

d. Scientists have hypothesized that the food quality is

a

d. Deduce the signific ance of these proteins being

better at Site1 than at Site2.

found in all of thespecies studied. [1]

v

Evaluate this hypothesis using the data provided. [2]

e. C alculate how many groups of LCC proteins are

2. The figure shows

E

a tripeptide. L abel one peptide bond

found in the prokaryote kingdom. [1]

in this molecule.

f. C alculate the percentage of groups analysed that

H O H O H
H O are found in the animal kingdom only. [1]

g. Deduce whether this data supports the hypothesis

N C C N C C N C C

that plants are moreclosely related to animals than

OH
H

H H H H H to prokaryotes. [2]

glycine glycine glycine

209
 B Fo r m and function

s
s
2 Cells

e
r
The form of a cell is its underlying shape and s t r u c t u re.

P
Fo r m s are often correlate d with function. Cells within

y
multicellular organisms are often specialized in their

l
s t r u c t u re. Their specialized structure corresponds to

n
their functions.

O
Some of the unique structures within a cell are not visible

i
using a light m i c ro s c o p e. These c an be observed using

s
the u l t ra - m a g n i f i c a t i o n of an ele ctron m i c ro s c o p e, thus

y
this level of structure is k n ow n as u l t ra s t r u c t u r e .
e

p
The background composite image is s h ow i n g Didinium
v

n as ut u m a tt a c k i n g a Pa r a m e c i u m . Didinium a tt a c k s with

organelles k n ow n as
o
t r i c h o c ys t s which h av e the ability
i
n

to t ra n s m i t a t ox i n as well as a tt a c h to the p r e y. Didinium

then engulfs its prey and ingests it. The Pa r a m e c i u m c an

U

be seen ejecting its ow n t r i c h o c ys t s to defend i t s e l f.

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v
E
B2.1 Membranes and membrane transport

How do molecules of lipid and protein assemble into biologic al membranes?

s
s
The liquid blobs in a lava lamp are a mixture of oils and

waxes, dissolved in a hydrophobic solvent. The other liquid,

e
through which the blobs rise and fall is water with a dye to

colour it. What prevents the two liquids from ever mixing?

r
Biologic al membranes form a exible frontier around every

y
cell, separating the water-based cytoplasm inside from

the water-based environment outside. Do you expect the

l
interior of membranes to be hydrophobic or hydrophilic?

n
Will the surfaces of the membrane be hydrophobic or

hydrophilic? What hydrophobic/hydrophilic properties are

t
needed for lipids and proteins in membranes?

O
i
s
▴ Figure 1 A lava lamp

y
e

p
What determines whether a substance c an pass through a biologic al membrane?
v

o
F ace masks are porous and allow particles
i

smaller than the pore size to pass through. What

n

particles must be able to pass through a dentist’s

mask? What size should the largest pores in a

dentist’s mask be if it was intended to exclude

U

virus particles? Biologic al membranes are very

n

sophistic ated and c an distinguish between

hydrophilic and hydrophobic particles. Which

o
d

type will pass through a membrane more easily?

Membranes c an discriminate between ions such

i

+ +
r

as Na , K and Cl and only allow ions needed by

t

the cell to enter. How could a membrane do this?

o

▴ Figure 2 Dentist wearing a surgic al mask

f

u
x

SL and HL AHL only

B2.1.1 Lipid bilayers as the basis of cell membranes B2.1.11 Relationships between fatty acid composition of
l
O

B2.1.2 Lipid bilayers as barriers lipid bilayers and their uidity

a

B2.1.3 Simple diusion across membranes B2.1.12 Cholesterol and membrane uidity in animal cells

B2.1.4 Integral and peripheral proteins in membranes B2.1.13 Membrane uidity and the fusion and formation of
v

B2.1.5 Movement of water molecules across membranes by vesicles

osmosis and the role of aquaporins B2.1.14 G ated ion channels in neurons
E

B2.1.6 Channel proteins for facilitated diusion B2.1.15 Sodium–potassium pumps as an example of

B2.1.7 Pump proteins for active transport exchange transporters

B2.1.8 Selectivity in membrane permeability B2.1.16 Sodium-dependent glucose cotransporters as an

B2.1.9 Structure and function of glycoproteins and example of indirect active transport

glycolipids B2.1.17 Adhesion of cells to form tissues

B2.1.10 Fluid mosaic model of membrane structure

211
 Form and function

B2.1.1 Lipid bilayers as the basis of

cellmembranes

Membranes are an essential component of cells. The plasma membrane forms

the border between a cell and its environment. Membranes inside eukaryotic

s
cells divide the cytoplasm into compartments. The basic structure of all biologic al

s
membranes is the same. A bilayer of phospholipids and other amphipathic

molecules forms a continuous sheet that controls the passage of substances

e
despite being 10 nanometres or less across. The structure of phospholipid

molecules and their arrangement into bilayers is described in Topic B1.1.

r
P

y
l
y

n
t

O
i
s
r

y
e

p
v

o
i
n

▸ Figure 3 Freeze-fracture electron

U

micrographs of cells show membranes

n

very clearly. In this image, a nuclear

membrane is visible at the top and below

it many membrane-bound vesicles and

o
d

cisternaethat divide the cytoplasm into

small compartments
i
r

t
o

B2.1.2 Lipid bilayers as barriers

f

Phospholipid molecules have a phosphate “head” and two hydroc arbon “tails”.
x

The tails of the phospholipids are hydrophobic and interact with each other to
l

form the core of biologic al membranes. Due to this, the membrane core has low
O

permeability to all hydrophilic particles, including ions withpositive or negative

charges and polar molecules such asglucose.

v

There are usually aqueous solutions on either side of cell membranes. These
E

solutions are in a liquid state, so both water molecules and hydrophilic solutes

are in continuous random motion. The solutes nearest to the membrane surface

might penetrate between the hydrophilic phosphate heads of the phospholipids,

but if they reach the hydrophobic core of the membrane they are drawn back

to the aqueous solution outside the membrane. The hydrophobic hydroc arbon

chains that form the core of the membrane do not repel hydrophilic solutes but

212
 Cells

they are more attracted to each other, and the solutes are much more attracted to

water outside the membrane.

Molecular size also inuences membrane permeability. The trend is that the larger

the molecule, the lower the permeability. For example, water molecules which

s
are only slightly larger than single oxygen atoms, pass through membranes more

easily than large molecules such as glycogen or protein.

s
hydrophobic hydrophilic

e
membrane phosphate heads on

core the surface of the

r
membrane

y
l
y

n
t

O
i
s
r

y
e

p
◂ Figure 4 The hydrophobic core of the membrane has
v

low permeability to polar molecules such as glucose (blue)

o
and charged particles such as chloride ions (green) so they
i

aqueous solution cytoplasm inside

c an be kept either in or out of a cell, whereas small non-polar
n

outside the cell the cell

molecules such as oxygen (red) c an pass through freely
U

Data-based questions: Membrane permeability

n

The graph in Figure 5 shows the energy level of six substances at dierent distances from the centre of a phospholipid

bilayer. Progesterone is a hormone and the other substances are drugs. Free energy is reduced by bond formation.
o
d

125

hydroc arbon tails hydrophilic water

i
r

100
heads
t
o

75
1

a
lom Jk /

ey
f

50 MM4
u
x

diaepam
Source: J. Phys.
ygrene

25

Chem. B 2017, 121,

theophylline
l

20, 5228–5237 April

O

0
a

2M 28, 2017

eerf

25 promaine
v

progesterone

50
E

75

0 1 2 3 4

distance from bilayer centre / nm

▴ Figure 5

213
 Form and function

1. Compare and contrast the energy levels of: 3. Using the diagrams and the graph, explain whether

hydroxyl ( OH) groups make molecules more or less

a. MMB4 and 2-PAM [2]

hydrophilic. [2]
b. promazine and progesterone [2]

4. Four membrane permeability c ategories have been

2. Deduce from the curves in the graph, which of the

s
dened: impermeable, low, medium, and high.
six substances is:

At least one of the ve drugs is in each c ategory.

s
a. most hydrophobic [2]

Suggest one drug for each c ategory. [4]

b. most hydrophilic [2]

e
5. Predict the permeability c ategory for

progesterone. [1]

r
P

y
l
B2.1.3 Simple diusion across membranes

n
Diusion is the spreading out of particles in liquids and gases that happens

t
bec ause the particles are in continuous random motion. More particles move

O
from an area of higher concentration to an area of lower concentration than move

i
in the opposite direction. There is therefore a net movement of particles from

s
the higher to the lower concentration—a movement down the concentration

r
gradient. Living organisms do not have to use energy to make diusion occur; it is

y
a passive process.
e

p
Simple diusion across membranes is due to particles passing between
v

phospholipids in the membrane. It c an only happen if the phospholipid bilayer

o
is permeable to the particles. Non-polar particles such as oxygen c an diuse
i

through easily. If the oxygen concentration inside a cell is reduced due to aerobic
n

respiration and the concentration outside is higher, oxygen will pass into the cell

through the plasma membrane by passive diusion.

U

The centre of membranes is hydrophobic, so ions with positive or negative

n

charges c annot easily diuse through. Polar molecules, which have partial

positive and negative charges over their surface, c an diuse at low rates between
o
d

the phospholipids of the membrane. Small polar particles such as urea or ethanol

pass through more easily than large particles.

i
r

the cornea has no blood supply so its cells obtain

t

oxygen by simple diffusion from the air

o

high concentration
f

of oxygen in the air

u

air
x

high concentration

fluid (tears)

of oxygen in the tears

l

cell on outer
O

▴ Figure 6 Model of diusion that coat the cornea

a

surface of the
with dots representing particles

cornea
v
E

oxygen passes through lower concentration

the plasma membrane by of oxygen in the cornea

simple diffusion cells due to aerobic respiration

▴ Figure 7 Passive diusion

214
 Cells

Data-based questions: Diusion of oxygen in the cornea

Oxygen concentrations were measured in the cornea of 1. C alculate the thickness of the rabbit cornea

anesthetized rabbits at dierent distances from the outer inmillimetres. [1]

s
surface. These measurements were continued into the

2. a. Describe the trend in oxygen concentrations

aqueous humor behind the cornea. The rabbit’s cornea

s
inthe cornea from the outer to the

is 400 micrometres (400 µm) thick. The graph in Figure

inner surface. [2]

e
8 shows the measurements. You may need to look at a

b. Suggest reasons for the trend in oxygen

diagram of eye structure before answering the questions.

concentration in the cornea. [2]

r
The oxygen concentration in normal air is 20 kilopasc als

(20 kPa). 3. a. Compare the oxygen concentrations in the

y
aqueous humor with the concentrations

20

in the cornea. [2]

l
b. Using the data in the graph, deduce if

n
aPk / negyxo

oxygendiuses from the cornea to the

aqueoushumor. [2]
15

O
4. Using the data in the graph, evaluate diusion

i
as a method of moving substances in large

s
fo

multicellular organisms. [2]

10
n o it a rt n e c n o c

y
5.e a. Predict the eect of wearing contact lenses

onoxygen concentrations in the cornea. [1]

p
b. Suggest how this eect could be minimized. [1]
v

6. The range bars for each data point indic ate how

much the
o
measurements varied. Explain the
i

reasonfor showing range bars on the graph. [2]

n

0 100 200 300 400

U

distance from outer surface of cornea/µm

◂ Figure 8
n
o
d

B2.1.4 Integral and peripheral proteins in

membranes
i
r

Bec ause of these varied functions, membrane proteins are very diverse in
o

structure and in their position in the membrane. They c an be divided into

a

twogroups.
f

• Integral proteins are hydrophobic on at least part of their surface and

x

are therefore embedded in the hydroc arbon chains in the centre of the
l

membrane. They may fit in one of the two phospholipid layers or extend
O

across both. M any integral proteins are transmembrane proteins—they

a

extend across the membrane, with hydrophilic parts projecting through the
v

regions of phosphate heads on either side.

• Peripheral proteins are hydrophilic on their surface, so are not embedded in

E

the membrane. Most of them are attached to the surface of integral proteins

and this attachment is often reversible. Some have a single hydroc arbon

chain attached to them which is inserted into the membrane, anchoring the

protein to the membrane surface.

215
 Form and function

Membranes all have an inner face and an outer face, and membrane proteins are

oriented so that they c an c arry out their function correctly. For example, pump

proteins in the plasma membranes of root cells in plants are oriented so that they

pick up potassium ions from the soil and pump them into the root cell.

s
The protein content of membranes is very variable bec ause the function of

membranes varies. The more active a membrane, the higher is its protein

s
content. Membranes in the myelin sheath around nerve bres just act as

e
insulators and have a protein content of about 18%. Most plasma membranes

on the outside of the cell have a protein content of about 50%. The highest

r
protein content—about 75%—is found in the membranes of chloroplasts and

mitochondria, which are active in photosynthesis and respiration.

y
l
y
B2.1.5 Movement of water molecules

n
acrossmembranes by osmosis and the role

O
of aquaporins

i
▴ Figure 9 The protein shown blue is a

s
receptor for the hormone EGF (epidermal
Water c an move in and out of most cells freely. Sometimes, the number of water

growth factor). It is an integral protein

molecules moving in and out is the same and there is no net movement. At other

y
bec ause it is embedded in the phospholipid

times, more molecules move in one direction or the other. This net movement

bilayer (orange = hydrophobic region and

e
isosmosis.

purple = hydrophilic). EGF, shown red, is

p
also a protein but as it binds to the exterior
Osmosis is due to dierences in the concentration of substances dissolved in
v

surface of the receptor, it is a peripheral

water (solutes). Substances dissolve by forming intermolecular bonds with water

rather than an integral protein.

o
i

molecules. These bonds restrict the movement of the water molecules. This

means that regions with a higher solute concentration have a lower concentration
n

of water molecules that are free to move than regions with a lower solute

concentration. Bec ause of this, there is net movement of water from regions
U

of lower solute concentration to regions with higher solute concentration. This

n

movement is passive bec ause no energy is directly expended to make it occur.

Osmosis c an happen in all cells bec ause water molecules, despite being
o
d

hydrophilic, are small enough to pass through the phospholipid bilayer. Some

cells have water channels c alled aquaporins, which greatly increase membrane
i
r

permeability to water. Examples are kidney cells that reabsorb water, and root
t
o

hair cells that absorb water from the soil.

a

At its narrowest point, the channel in an aquaporin is only slightly wider than
f

water molecules, which therefore pass through in single le. Positive charges at
x

this point in the channel prevent protons (H ) from passing through.

l
O

a
v
E

▴ Figure 10 Structure of an aquaporin

216
 Cells

(a)

B2.1.6 Channel proteins for facilitated

diusion

Ions and polar molecules c annot easily pass between phospholipids, but

diusion of these substances across a membrane is still possible with the help

s
of proteins acting as channels. A channel protein is an integral, transmembrane

s
protein with a pore that connects the cytoplasm to the aqueous solution outside

the cell. The diameter of a pore and the chemic al properties of its sides ensure

e
that only one type of particle passes through—for example, sodium ions or (b)

potassium ions, but not both.

r
membrane

P
Channel proteins allow particles to pass through in either direction, but more

y
pass from the higher to the lower concentration than vice versa. There is cytoplasm

therefore a net movement from the higher concentration to the lower. No energy

l
is expended by the cell to c ause this movement, so it is a type of diusion.

n
It is c alled facilitated diusion bec ause channel proteins are required for the

t
movement to occur. Simple diusion here would be movement between

O
phospholipid molecules in the membrane.

i
s
Cells c an select which hydrophilic substances diuse in and out by the types

of channel that are synthesized and placed in the plasma membrane. Some
▴ Figure 11 M agnesium channel viewed

y
from the side and from the outside of the
channels c an be opened and closed, so permeability c an be temporarily

membrane. The structure of the protein

e
changed when necessary.

p
making up the channel ensures that only

magnesium ions c an pass through the pore

v

in the centre

B2.1.7 Pump proteins for active transport

o
i
n

Cells absorb some substances, even though the concentration inside is already

higher than outside. The substance is absorbed against the concentration

gradient. Less commonly, cells sometimes pump substances out even though
U

there is already a higher concentration outside. Pump proteins in the membrane

n

c arry out these transport tasks. Pump proteins dier in three ways from channel

proteins in how they transport particles across membranes:

o
d

• pump proteins use energy so they c arry out active transport, whereas

diffusion through channel proteins is passive

i
r

• pump proteins only move particles across the membrane in one direction,
t
o

whereas particles c an move in either direction through a channel protein

a

• pump proteins usually move particles against the concentration gradient,

f

whereas facilitated diffusion through channel proteins is always down the

u
x

concentration gradient.
l

Pump proteins are interconvertible between two dierent conformations. In

O

one conformation, the transported particle c an enter the pump from one side of

the membrane to reach a central chamber or a binding site. The pump protein
v

then changes to the other conformation, which allows the ion or molecule to

pass out on the opposite side of the membrane. The pump protein returns to
E

its original conformation. Energy is used to change the protein from one of the

conformations (the more stable) to the other (the less stable), but the reverse

change does not require energy. Most pump proteins use ATP to supply

the energy required for active transport. Every cell produces its own ATP by

cellrespiration.

▴ Figure 12 Action of a pump protein that

transports Vitamin B into Escherichia coli

12

217
 Form and function

The membranes of cells contain many dierent pump proteins, each of which

transfers one specic type of particle across the membrane. This allows the cell

to control the content of its cytoplasm precisely. It also allows specic solutes

required by a cell to be absorbed even when they are in very low concentrations

in the environment.

s
s
Data-based questions: Phosphate absorption in barley roots

e
Roots were cut o from barley plants and used to An experiment was done to test which method of

r
investigate phosphate absorption. Roots were placed membrane transport was used by the roots to absorb

P
in phosphate solutions and air was bubbled through. phosphate. Roots were placed in the phosphate solution

y
The phosphate concentration was the same in each as before, with 21.0% oxygen bubbling through. Varying

c ase, but the percentages of oxygen and nitrogen were concentrations of a substance c alled DNP were added.

l
y
varied in the air bubbled through. The rate of phosphate DNP blocks the production of ATP by aerobic cell

n
absorption was measured. Table 1 shows the results. respiration. Figure 13 shows the results of the experiment.

O
Oxygen Nitrogen Phosphate absorption/
0.4

i
–1 –1

/% /% μ mol g h

s
0.3

0.1 99.9 0.07

phosphate

r
absorption

y
0.3 99.7 0.15 0.2

1 1
/μmol g h
e
0.9 99.1 0.27

0.1

p
2.1 97.1 0.32
v

21.0 79.0 0.33

o
0 2 4 6 8 10
i

3
DNP concentration / mmol dm

▴ Table 1
n

1. Describe the eect of reducing the oxygen ▴ Figure 13 Eect of DNP concentration on phosphate absorption

concentration below 21.0% on the rate of

U

3. Deduce, with a reason, whether the roots

phosphateabsorption by roots. You should only

n

absorbedthe phosphate by diusion or by

useinformation from Table 1 in your answer. [3]

activetransport. [2]

2. Explain the eect of reducing the oxygen

o
d

4. Discuss the conclusions that c an be drawn

concentration from 21.0% to 0.1% on phosphate

from thedata in the graph about the method of

absorption. In your answer, you should use as

i
r

membranetransport used by the roots to absorb

muchbiologic al understanding as possible of

t

phosphate. [2]
o

howcells absorb mineral ions. [3]

a
f

u
x

B2.1.8 Selectivity in membrane permeability

l

A semi-permeable membrane allows the passage of certain small solutes and is

O

freely permeable to the solvent. This describes articial membranes of the type that

are used for kidney dialysis, but it does not match the permeability properties of cell
v

membranes, which show more selectivity and have variable permeability to water.
E

A selectively permeable membrane allows the passage of particular particles, but

not others. F acilitated diusion and active transport allow selective permeability

bec ause channel proteins and pump proteins are specic to particular particles.

A chloride channel, for example, allows only chloride ions to diuse across the

membrane. However, simple diusion is not selective and depends only on the

size and polarity of particles. Small hydrophobic particles c annot be prevented

from passing across cell membranes.

218
 Cells

Bec ause cell membranes are partly semi-permeable and partly selectively

permeable, they are sometimes described as partially permeable—all three of

these terms are widely used.

s
B2.1.9 Structure and function of

s
glycoproteins and glycolipids

e
Glycoproteins are conjugated proteins with c arbohydrate as the non-

r
polypeptide component. They are a component of the plasma membrane of

cells, with the protein part embedded in the membrane and the c arbohydrate

y
part projecting out into the exterior environment of the cell.

Glycolipids are molecules consisting of c arbohydrates linked to lipids. The

l
y
c arbohydrate part is usually a single monosaccharide or a short chain of between

n
two and four sugar units. The lipid part usually contains one or two hydroc arbon

t
chains, which naturally t into the hydrophobic core of membranes. Glycolipids

O
occur in the plasma membranes of all eukaryotic cells, with the attached

i
c arbohydrate projecting outwards into the extracellular environment of the cell.

s
The role of glycoproteins in cell-to-cell recognition is described in Section B1.1.7.

y
Glycolipids also have a role in cell recognition. They help the immune system to
e
distinguish between self and non-self cells, so pathogens and foreign tissue c an

p
be recognized and destroyed. Glycoproteins and glycolipids together form a
v

c arbohydrate-rich layer on the outer face of the plasma membrane of animal cells,

o
with an aqueous solution in the gaps between the c arbohydrates. This layer is
i

c alled the glycoc alyx. The glycoc alyx of adjacent cells c an fuse, binding the cells
n

together and preventing the tissue from falling apart.

U

n
o
d

i
r

t
o

a
f

u
x

l
O

◂ Figure 14 The glycoc alyx of

endothelium cells in blood c apillaries

v

projects into the lumen. In this brain

c apillary the glycoc alyx is particularly dense

E

and forms part of the blood–brain barrier.

It prevents plasma cells and circulating

proteins from binding to the c apillary wall,

which reduces the chance of inammation

and blood clotting.

219
 Form and function

B2.1.10 Fluid mosaic model of membrane

structure

Several models of membrane structure have been proposed but one particular

model is now so strongly supported by evidence that it is unlikely to be replaced.

s
In this model, there is a bilayer of phospholipids with proteins in a variety of

s
positions. Peripheral proteins are attached to the inner or outer surface. Integral

proteins are embedded in the phospholipid bilayer, in some c ases with parts

e
protruding on one or both sides. The proteins are likened to the tiles in a mosaic.

Bec ause the phospholipid molecules are free to move laterally in each of the

r
two layers of the bilayer, the proteins c an also move. This gives the model its

y
name—the uid mosaic model.

l
saturated hydrocarbon chains have
pore cholesterol

y
straight chains whereas
through embedded in

n
carbohydrate unsaturated chains carbohydrate part
channel the hydrophobic

t
part of a glycolipid have kinks of a glycoprotein
protein core of the membrane

O
i
s
hydrophilic

y
phosphate

head of
e

p
phospholipid
v

hydrophobic tails

of phospholipids
o
i

phospholipid
(unsaturated
n

bilayer (about
hydrocarbon

8nm
chains would
U

have kinks)
n
o
d

integral proteins peripheral proteins

i

embedded in the attached to the

r

bilayer with a membrane surface

t
o

transmembrane
a

protein on the left

f

▴ Figure 15 Fluid mosaic model of membrane structure

x

l
O
LHA

B2.1.11 Relationships between fatty acid

a

composition of lipid bilayers and their uidity

v

S aturated fatty acids have straight chains and therefore pack together tightly in
E

bilayers, giving a high density of phospholipids. This reduces the uidity of the

membrane and therefore its exibility and permeability by simple diusion. In

contrast, unsaturated fatty acids have one or more kinks in their hydroc arbon

chain, so they pack together more loosely. This makes the membranes more

uid, exible and permeable.

220
 Cells

LHA
Relative amounts of saturated and unsaturated fatty acids are regulated so that

the membranes have the required properties. They must remain uid but be

strong enough to avoid becoming perforated. They must be permeable but not

too porous. The ideal ratio of saturated to unsaturated fatty acids depends on

the temperatures that a cell experiences. For example, sh from Antarctic waters

s
have been found to have a higher percentage of unsaturated fatty acids in their

membranes than sh from warmer waters.

s
e
r
P

y
l
y
▴ Figure 16 A membrane containing only saturated fatty acids (le) is thicker, more

n
viscous, has a higher density of phospholipids and a higher melting point than a membrane

t
containing both saturated and unsaturated fatty acids (right)

O
i
s
Data-based questions: Frost hardiness and double bonds in chickpeas

y
Freezing temperatures c ause cytoplasm to leak out of The proportions of saturated and unsaturated membrane
e
leaf cells in chickpea plants (Cicer arietinum). This kills lipids were measured aer the treatments (double bond

p
the cells. The eectiveness of two treatments preventing index). Frost hardiness was assessed by nding the
v

leakage was investigated. The treatments were: temperature that killed 50% of leaf cells. The graph in

Figure 17 shows
o
the results.
i

• acclimatization of plants by keeping them at

temperatures close to freezing point for two weeks 1. a. State the relationship between LT and
n

50

doublebond index. [1]

• spraying the outside of the leaves with ABA, a

b. Explain the relationship. [2]

hormone produced by plants in response to stress.
U

2. Using only the data in the graph, outline the

3.0

2 weeks warm no 

eects of ABA on the chickpea plants. [2]

2 weeks warm  alied

2.8
o
d

2 weeks old no  3. Deduce the eects of cold treatment on the

xedni dnob

2 weeks old  alied

proportions of saturated and unsaturated

2.6
i

membranelipids in chickpea plants. [2]

r

2.4
4. Gardeners are advised to “harden o ” plants that
o
elbuod

have been raised in a warm greenhouse before

2.2

planting them outside in colder conditions. Discuss

f

whether spraying with ABA or 2 weeks of cold

2.0
x

acclimatization is likely to be more eective. [3]

l

1.8
O

–18 –16 –14 –12 –10 –8 –6

a

LT (C)
50
v

▴ Figure 17
E

221
 Form and function
LHA

B2.1.12 Cholesterol and membrane uidity

in animal cells

Cholesterol makes up between 20% and 40% of the lipids in

CH CH CH CH
3 2 2 3
the plasma membranes of eukaryotes. It is a steroid rather than

s
a glyceride. Most of a cholesterol molecule is hydrophobic

CH CH CH
2

s
so it is attracted to the hydrophobic hydroc arbon tails in the
CH
3

CH centre of the membrane, but one end of the molecule has a

e
3

hydroxyl ( OH) group which is hydrophilic. This is attracted to the

CH
3 phosphate heads on the periphery. Cholesterol molecules are

r
therefore positioned between phospholipids in the membrane,

y
with the hydroxyl group usually facing outwards. It preferentially

interc alates between saturated rather than unsaturated

l
HO
hydroc arbon chains.

n
hydrophilic hydrophobic
The uidity of membranes needs to be c arefully controlled. If

t
membranes were too uid, they would be less able to control

▴ Figure 18 The structure of cholesterol

O
what substances pass through. If they were too viscous and

i
inexible, cell movement would be restricted and the cell would be more likely

s
to burst. Cell membranes do not correspond exactly to any of the three states of

r
matter—they are in what is c alled a liquid-ordered phase. The lipid molecules are

y
packed densely but are still free to move laterally. Cholesterol helps to maintain
e
the necessary orderly arrangement of phospholipids. Cholesterol therefore

p
stabilizes membranes at higher temperatures, maintaining impermeability to
v

hydrophilic particles such as sodium ions and hydrogen ions. Cholesterol also

helps to ensure that saturated fatty acid

o
tails do not solidify at low temperatures,
i

so preventing a stiening of themembrane.

n

ENDOCYTOSIS
U

B2.1.13 Membrane uidity and the fusion

n

cell interior
and formation of vesicles
o
d

A vesicle is a small sac of membrane with a droplet of uid inside. Vesicles are

exterior

spheric al and most eukaryotic cells contain them. They are a very dynamic feature
i
r

of cells as there is a continuous cycle of making vesicles, moving them within

t

the cell to transport their contents and then unmaking them. This c an happen
o

bec ause of the uidity of membranes, which allows structures surrounded by a

a

membrane to change shape and move.

f

To make a vesicle, a small region of a membrane is pulled from the rest of the
x

membrane and is pinched o. Proteins in the membrane carry out this process,
l

using energy from ATP. If a vesicle is made from the plasma membrane by pinching
O

a small piece of it inwards, the vesicle will contain material that was outside the

cell. This is method of taking materials into the cell and is calledendocytosis.
v

Vesicles made by endocytosis contain water and solutes from outside the cell.
E

Oen, they contain larger molecules needed by the cell that c annot pass across

the plasma membrane. For example, in the placenta, proteins from the mother ’s

blood, including antibodies, are absorbed into the foetus by endocytosis. Some
vesicle

cells take in large undigested food particles by endocytosis. This happens in

unicellular organisms including Amoeba and Paramecium. Some types of white

blood cell take in pathogens including bacteria and viruses by endocytosis and

▴ Figure 19 Formation of a vesicle by

then kill them. This is part of the body’s response to infection.

endocytosis

222
 Cells

LHA
Vesicles c an be used to move materials around inside cells. In some c ases, it is

the contents of the vesicle that need to be moved. In other c ases, it is proteins in

the membrane of the vesicle that need to be moved. An example of moving the

vesicle contents occurs in secretory cells. Protein is synthesized by ribosomes on

the rough endoplasmic reticulum (rER) and accumulates inside the rER. Vesicles

s
containing the proteins bud o the rER and c arry them to the Golgi apparatus.

s
When they have reached their destination, vesicles fuse with a target membrane

e
and disappear in the process. This has the eect of transferring all the contents of

a vesicle across the membrane. If a vesicle fuses with the plasma membrane, the

r
contents are expelled from the cell. This process is c alled exocytosis.

P
Exocytosis c an also be used to expel waste products or unwanted materials. An EXOCYTOSIS

y
example is the removal of excess water from the cells of unicellular organisms.

l
The water is loaded into a vesicle, sometimes c alled a contractile vacuole,

y
which is then moved to the plasma membrane for expulsion by exocytosis.

n
vesicle

Polypeptides that have been processed in the Golgi apparatus are c arried to the

t
plasma membrane in vesicles for exocytosis. In this c ase, the release is referred to

O
as secretion, bec ause a useful substance is being released, not a waste product.

i
Digestive enzymes and protein hormones are secreted in this way. exterior

s
r

y
e

p
v

o
i
n

C
U

n
o
d

i
r

▴
t

Figure 20 Fusion of a vesicle with the

o

membrane in exocytosis
a
f

u
x

▴ Figure 21 The large vesicle in the centre of this Amoeba is a contractile vacuole. There
O

are also many food vacuoles in the cytoplasm of the cell

In a growing cell, the area of the plasma membrane needs to increase.

v

Phospholipids are synthesized and then inserted into the rER membrane.

Ribosomes on the rER synthesize membrane proteins which are added to the
E

membrane. Vesicles bud o the rER and move to the plasma membrane. They

fuse with it, each increasing the area of the plasma membrane by a very small

amount. The same method is used to increase the size of organelles such as

mitochondria in the cytoplasm.

223
 Form and function
LHA

vesicles bud off from

proteins are synthesized vesicles bud off from the Golgi the Golgi apparatus

by ribosomes and then the rER and carry the apparatus and carry the modified

enter the rough proteins to the Golgi modifies the proteins to the plasma

endoplasmic apparatus proteins membrane

s
reticulum

EXOCYTOSIS

s
ENDOCYTOSIS

vesicles fuse

e
part of the plasma
with the plasma

membrane is pulled inwards

membrane

r
a droplet of fluid becomes the contents of

P
enclosed when a vesicle is the vesicle are

y
pinched off expelled

l
vesicles can then move the membrane

y
then flattens

n
through the cytoplasm

carrying their contents out again

O
▴ Figure 22 Vesicle movements in a cell

i
s
r
B2.1.14 Gated ion channels in neurons

y
e
Ion channels allow specic ions to pass across a membrane in either direction,

p
resulting in a net movement from the higher to the lower concentration of the ion.
v

This type of membrane transport is facilitated diusion. Gated ion channels are

o
able to open and close reversibly, allowing diusion to be switched on and o.
i

This is particularly useful in neurons (nerve cells) where there are voltage-gated
n

sodium and potassium channels along nerve bres and neurotransmitter-gated

channels at synapses.
U

Voltage-gated sodium and potassium channels

n

A nerve impulse involves rapid movements of sodium and potassium ions across

a neuron’s membrane. These movements occur by facilitated diusion through

o
d

sodium and potassium channels, both of which are voltage gated. Voltages

across membranes are due to an imbalance of positive and negative charges

i
r

across the membrane. A negative voltage indic ates that there are relatively more
t

positive charges outside the neuron than inside. If the voltage is below −50 mV,
o

sodium and potassium channels remain closed. If it rises above −50 mV sodium

channels open, allowing sodium ions (Na ) to diuse in. This c auses the voltage
f

to rise more. When it reaches +40 mV, potassium channels open, allowing
x

potassium ions (K ) to diuse out of the neuron.

l
O

The gating mechanism of both sodium and potassium channels involves

a

reversible conformation changes with subunits. The subunits c an be in either an

open position with a narrow pore between them that allows ions to pass or in a
v

closed position with no pore. The potassium channel has four subunits and an

extra globular protein subunit that resembles a ball, attached by a exible chain
E

of amino acids. When the four subunits are in the open conformation, the ball

c an t inside the open pore and does so within milliseconds of the pore opening.

The ball remains in place until the potassium channel returns to its original closed

state. There may be a similar mechanism in the sodium channel.

+ +

Sodium and potassium channels must be specic, despite Na and K ions

both c arrying a single positive charge. Sodium channels allow Na ions to pass

224
 Cells

LHA
+ +

through but not the larger K ions. Potassium channels do not allow Na ions to

pass through. The pore in a potassium channel is 0.3 nm wide at its narrowest.

Potassium ions are slightly smaller than 0.3 nm but when they dissolve, they

become bonded to a shell of water molecules. This makes them too large to

pass through the pore. To pass through, the bonds between the potassium ion

s
and the surrounding water molecules are broken and bonds form temporarily

between the ion and a series of amino acids in the narrowest part of the pore.

s
Aerthe potassium ion has passed through this part of the pore, it c an again

e
become associated with a shell of water molecules. Sodium ions are too small to

form bonds with the amino acids in the narrowest part of the pore, so they c annot

r
shed their shell of water molecules.

y
net negative charge
1 channel closed 2 channel briefly open

l
+ + + + + + + + outside

y
+

n
+
+
+
+
+
+
+

O
i
+
+
+ +
+ + +
+

s
inside of axon
‒ ‒ ‒ ‒ ‒ ‒ ‒ ‒ ‒

chain

r
net negative charge inside

y
+ net positive
K ions
ball the axon and net positive
e
charge

charge outside

p
v

3 channel closed by "ball and chain"

o
i
n

+ +

+ +

+ +
U

+ +
n
o
d

hydrophobic core hydrophilic outer

i
r

◂ Figure 23 Voltage-gating

of the membrane parts of the membrane

t

of potassium channels
o

a
f

Nicotinic acetylcholine receptors

u

Acetylcholine is the neurotransmitter in many synapses. At these synapses, there

x

are receptors for acetylcholine. But both nicotine and acetylcholine bind to the
l

receptors, hence they are c alled nicotinic acetylcholine receptors.

O

These receptors have ve transmembrane subunits arranged symmetric ally, with
v

a binding site between two of the subunits for acetylcholine. Binding c auses a

conformational change, which opens a pore between the ve subunits, through
E

which c ations (positively charged ions) including sodium c an pass. Sodium

diuses into the postsynaptic neuron, changing its voltage and c ausing voltage-

gated sodium channels to open. Binding of acetylcholine is reversible. When it

dissociates from the receptor, the conformational change c aused by binding is

▴ Figure 24 Nicotinic acetylcholine

reversed and the pore in the receptor is closed.

receptor with acetylcholine bound (red) and

the c ation pore open

225
 Form and function
LHA

Activity: Sketching the nicotinic acetylcholine receptor

Figure 24 on the previous page shows the structure of a nicotinic acetylcholine receptor viewed from the outside of the

plasma membrane. Sketch this protein in side-view within the membrane, to show the structure and position that you

s
expect it to have, then check whether your sketch matches the actual structure by going online to the PDB Molecule of

the Month website (molecule code number 2BG9).

s
e
B2.1.15 Sodium–potassium pumps as an

r
example of exchange transporters

y
For a neuron to convey a nerve impulse there must be concentration gradients

of sodium and potassium ions across the membrane. These are generated by

l
active transport, using a sodium–potassium pump protein. This pump follows a

n
repeating cycle of steps that result in three sodium ions being pumped out of the

axon and two potassium ions being pumped in. E ach time the pump goes round

t
this cycle it uses one ATP to supply energy.

O
i
This pump is an example of an exchange transporter bec ause it transports

s
dierent ions in opposite directions across the membrane. In neurons, this helps

r
to generate a charge imbalance and therefore a membrane potential, which is a

y
voltage across the membrane.
e

p
1 2 3
v

o
i
n

C
U

p p
n

ATP

ADP

The pump is open ATP transfers a The pump opens

o
d

to the inside, so three phosphate group to the outside and

+ +
Na ions can enter and to the pump which the Na ions can
i
r

attach to their binding causes a conformational exit, increasing the

t

+ +
sites, reducing the Na change and closes Na concentration
o

concentration inside the pump outside the neuron

a

4 5 6
f

u
x

l
O

a
v

p
E

+ +
Two K ions from Binding of K The pump opens

outside enter and attach causes release of the to the inside and the

+
to their binding sites in phosphate group, K ions can exit,

+
the pump, reducing the which causes a increasing the K

+
K concentration outside conformational concentration inside;

+
change and closes more Na ions can
▸ Figure 25 The sodium–potassium pump

the pump then enter

226
 Cells

LHA
B2.1.16 Sodium-dependent glucose

cotransporters as an example of indirect

active transport

s
Sodium–glucose cotransporter proteins transfer a sodium ion and a glucose

molecule together across a plasma membrane into a cell. The glucose molecule

s
c an move against its concentration gradient bec ause the sodium ion is moving

e
down its concentration gradient. The energy released by the movement of the

sodium ion is greater than the energy needed to move the glucose.

r
Sodium-dependent cotransport is used by cells in the wall of the proximal tubule

y
in the kidney. These cells reabsorb glucose that has been ltered out the blood to

prevent it being lost in urine.

l
+

y
Glucose absorption into cells depends on the Na ion concentration being

n
greater outside than inside. The concentration gradient is maintained by

t
active transport of Na ions out of the cell. Sodium–potassium pumps in the

O
+

plasma membrane on the inner (basal) side of the cell transfer Na out of the

i
+

cell towards nearby blood c apillaries and transfer K in. Sodium-dependent

s
glucose cotransport depends on energy from ATP, so it is not passive. However,

r
it is not typic al active transport bec ause the energy is not used directly by the

y
cotransporter. This is c alled indirect or secondary active transport.
e

p
outer membrane cytoplasm with
v

+
inner membrane
of cell with Na high glucose and

o
+
of cell with
dependent glucose low Na
i

+ +
Na / K pumps
transporters concentrations
n

C
U

n
o
d

i
r

blood in endothelium cells tissue

t

◂ Figure 26 Glucose uptake into a cell

o

capillary forming the wall of a fluid

by cotransport
a

blood capillary between

f

cells
u
x

l
O

B2.1.17 Adhesion of cells to form tissues

a

Cells in a tissue are linked by cell-to-cell junctions. These junctions depend on

v

cell-adhesion molecules (CAMs) in the plasma membranes of adjacent cells.

A range of CAMs is found in dierent types of cell junction. CAMs are typic ally
E

proteins with some domains embedded in the phospholipid bilayer and others

protruding outwards into the extracellular environment. A junction is formed by

the CAMs in adjacent cells binding together their extracellular domains. In some

c ases, the same type of CAM is present in both cells and these bind together to

▴ Figure 27 If Hydra is broken up into

build a group of cells of the same type. In other c ases, the CAMs are dierent and
single cells, the cells reaggregate into

an asymmetric al junction is formed. This is useful in linking dierent cell types to

tissues by cell-to-cell adhesion, with the

form a more complex structure.

tissues arranging to form a new polyp

227
 Form and function
LHA

plasma plasma

membrane cadherin molecules membrane

of Cell A bonded together of Cell B

s
s
e
r
P

y
cytoplasm narrow intercellular cytoplasm

l
y
of Cell A space with tissue fluid of Cell B

n
▴ Figure 28 Cell-to-cell adhesion

O
i
Cell adhesion maintains the architecture of tissues and organs. It is needed for

s
functional relationships between adjacent cells. Some types of junction prevent

extracellular movement of substances in a tissue and other types facilitate it. Cell

y
adhesion has major roles in the immune system. In tumours, it prevents cells from
e
becoming separated and migrating to form secondary tumours, so it prevents

p
malignancy spreading (metastasis).
v

o
i

Linking questions
n

1. What processes depend on active transport in biologic al systems?

U

a. Outline the role of active transport in the generation of root pressure

n

in plants. (B3.2.16)

b. Explain the role of auxin eux c arriers in maintaining concentration

o
d

gradients of phytohormones. (C3.1.20)

c. Describe how active transport plays a role in osmoregulation by the

i
r

loop of Henle. (D3.3.9)

t
o

2. What are the roles of cell membranes in the interaction of a cell with its
a

environment?
f

a. Describe the role of the cell surface inactivation of B-lymphocytes by

x

helper T-lymphocytes. (C3.2.8)

l

b. Outline one example of the role of glycolipids in cell-to-cell

O

recognition. (B1.1.7)

c. Explain the process of tyrosine kinase activation. (C2.1.11)

v
E

228
B2.2 Organelles and compartmentalization

How are organelles in cells adapted to their functions?

s
s
A shoemaker who works by hand has many dierent

tools. E ach tool has a structure that makes it well

e
suited to c arry out a specic task such as cutting

leather, making holes, or stitching the shoe together.

r
What is the advantage of specialization in tools?

y
E ach organelle in a eukaryotic cell is specialized for a

particular function and is adapted to the function by its

l
structure. In what ways is the tool kit of a shoemaker

n
similar and in what ways is it dierent from the

organelles within a cell? How do tools evolve? Is the

t
evolution of tools similar to the evolution of cells?

O
i
s
▴ Figure 1 Shoemaker ’s tools

y
e

p
What are the advantages of compartmentalization in cells?
v

o
Compartmentalization must have signic ant
i

advantages to justify the large quantities of energy

n

needed to construct the 100,000 compartments

in a bee colony. What advantages does

U

compartmentalization provide to the bee colony?

What are the advantages of storing faeces, pollen,

n

honey and larvae in dierent compartments?

Compartmentalization also has great benets

o
d

in eukaryotic cells. What are some examples of

compartmentalized functions in eukaryotic cells? What

i
r

is the dierence between the comb constructed by

t

honeybees and the compartments of eukaryotic cells?

o

▴ Figure 2 Honeybees construct wax comb with

f

hexagonal compartments that are used for storage of pollen

x

or honey and protection for worker larvae and pupae

l
O

SL and HL AHL only

B2.2.1 Organelles as discrete subunits of cells that are B2.2.4 Adaptations of the mitochondrion for production of
v

adapted to perform specic functions ATP by aerobic cell respiration

B2.2.2 Advantage of the separation of the nucleus and B2.2.5 Adaptations of the chloroplast for photosynthesis
E

cytoplasm into separate compartments B2.2.6 Functional benets of the double membrane of the

B2.2.3 Advantages of compartmentalization in the nucleus

cytoplasm of cells B2.2.7 Structure and function of free ribosomes and of the

rough endoplasmic reticulum

B2.2.8 Structure and function of the Golgi apparatus

B2.2.9 Structure and function of vesicles in cells

229
 Form and function

B2.2.1 Organelles as discrete subunits of

cells that are adapted to perform specic

functions

s
Organelles are discrete structures in cells that are adapted to perform one or

more vital functions. Organelles are ecient bec ause they are specialized for a

s
limited range of functions. Eukaryotic cells have many organelles. Their structure

e
and their appearance in electron micrographs are described in Section A2.2.10.

In some c ases a single membrane or double membrane encloses the uid

r
contents of an organelle. In other c ases the organelle is a solid structure, largely

composed of proteins or RNA, and it is not membrane-bound (Table 1).

y
No membrane Single membrane Double membrane

l
y
Ribosomes Vesicles and vacuoles Nuclei

n
Centrioles Rough endoplasmic reticulum Mitochondria

t
Microtubules Smooth endoplasmic reticulum Chloroplasts

O
i
Proteasomes Golgi apparatus Amyloplasts

Nucleoli Lysosomes Chromoplasts

s
▴ Table 1 Examples of organelles in eukaryotic cells

y
Nuclei, vesicles, ribosomes and the plasma membrane are all organelles. Some
e

p
other structures are not considered to be organelles:
v

• cell walls are outside the plasma membrane so are extracellular structures

o
rather than organelles

▴ Figure 3 Cells in ripe tomato fruits

i

• cytoskeletons consist of narrow protein filaments spread through much of the

contain chromoplasts that give the fruit

n

cell so are not discrete enough to be an organelle

a bright red colour. Chromoplasts are

• cytoplasm is not a discrete structure as it includes many different structures

double membraned and contain DNA. They
U

develop from chloroplasts when the seeds and performs many functions.
n

in the tomato fruit are mature and ready

Prokaryotic cells have fewer organelles than eukaryotes. This could be bec ause
to be dispersed. Chlorophyll is replaced

their cells are smaller or bec ause they concentrate on a more limited range of
by red pigments. Red coloration attracts
o
d

functions. It may also allow functions to be integrated and therefore c arried out
animals that feed on the fruits and disperse

the seeds more rapidly—for example, transcription and translation.

i
r

t
o

Thinking skills: Applying criteria for judgement

a

ATL
f

Do you think these organelles are part of the cytoplasm ways is this denition useful? How does it aect your
u
x

ornot? answer to (a) and (b)?

a. vacuoles in plant cells Another denition of the cytoplasm is the thick solution
l
O

that lls each cell and is enclosed by the cell membrane.

a

b. mitochondria and chloroplasts

The organelles are embedded in the cytoplasm. In what

During cell division, mitosis refers to the division of

ways is this denition useful? How does this denition
v

the nucleus and cytokinesis refers to the division of the

aect your answer to (a) and (b)?

cytoplasm. Does the duplic ation of mitochondria and

E

Discuss the statement: “The criteria for judgement we use

chloroplasts constitute a third process? What happens to

aect the truth of the knowledge claims we make.”

plant vacuoles during cytokinesis?

One denition of the cytoplasm is everything enclosed

by the plasma membrane excluding the nucleus. In what

230
 Cells

Experimental techniques: Dierential centrifugation

Separating cells into types of organelle is c alled cell sucrose solution are placed in the centrifuge tube.

fractionation. The rst stage is to mix the cells with Centrifugation at high speed (62,000 g) c auses the

s
ice-cold extraction buer. The cold temperature slows chromoplasts to become concentrated between the

−3 −3

down degeneration and the buer prevents problems 0.9 mol dm and 1.45 mol dm sucrose layers. Only

s
c aused by pH dierences and osmosis. The mixture is when such protocols are developed c anthere be rapid

e
then gently blitzed in a scientic version of a food blender progress in determining and investigating the functions

to burst open the cells and release the organelles. The of individual organelles. This is an exampleof progress in

r
resulting homogenate is ltered to remove whole cells science following development of newtechniques.

and other structures larger than organelles. It is then

y
centrifuged and bec ause organelles are denser than

the extraction buer, they sediment to the bottom of the

l
centrifuge tube to form a “pellet”. The remaining liquid,

n
c alled the supernatant, is disc arded. The pellet is mixed

with another solution to resuspend the organelles.

O
This new mixture is then centrifuged again, with the

i
speed and duration c arefully chosen so that the required

s
organelles separate from everything else. This is c alled

dierential centrifugation. L arger organelles sink to

y
the bottom of the tube at a faster rate and at lower
e
centrifugation speeds than smaller organelles.

p
The density of the liquid c an be varied to separate
v

organelles of dierent density. For example, to separate

chromoplasts from other organelles in tomato cells, three ▴ Figure 4

o
Ultracentrifuge tubes are spun at high revolutions
i

−3 −3 −3
per minute by a rotor
layers of 0.5 mol dm , 0.9 mol dm and 1.45 mol dm
n

B2.2.2 Advantage of the separation of

U

the nucleus and cytoplasm into separate

compartments
o
d

In eukaryotes, keeping chromosomes inside the nucleus safeguards the DNA.

i

Eukaryotes gain another advantage in having the nucleus and cytoplasm as

r

separate compartments. In prokaryotic cells, there is no nucleus, so DNA and

t
o

ribosomes are together in the cytoplasm and translation c an happen immediately

a

aer transcription. In eukaryotic cells, translation c annot begin until messenger

f

RNA (mRNA) has passed out of the nucleus via the pores in the nuclear
u
x

membrane. This allows mRNA to be modied aer it has been produced by

transcription in the nucleus, but before it is translated. The process is c alled post-
l

transcriptional modic ation and is described in more detail (for HL only) inSection
O

D1.2.15, and both transcription and translation are described (for SL and HL) in

Topic D1.2
v

◂ Figure 5 In this electron micrograph of part of a prokaryotic

E

cell, the arrow points to an RNA polymerase attached to a strand of

DNA at the point where transcription of a gene is initiated. The black

spheric al structures are ribosomes. They are translating the mRNA

produced by a series of RNA polymerases that are moving to the right

along the DNA. This image shows that translation c an begin before

transcription of a gene has been completed in prokaryotes

0.5 µm

231
 Form and function

B2.2.3 Advantages of compartmentalization

in the cytoplasm of cells

The cytoplasm of eukaryotic cells is divided into compartments by membrane-

bound organelles. There are several advantages of being compartmentalized.

s
food vacuoles

• Enzymes and substrates for a particular process c an be much more

s
concentrated than if they were spread throughout the cytoplasm.

e
• Substances that could c ause damage to the cell c an be kept inside the

membrane of an organelle. For example, the digestive enzymes of a

r
lysosome could digest and kill a cell, if they were not safely stored inside the

lysosome membrane.

y
• Conditions such as pH c an be maintained at an ideal level for a particular

contractile

l
process, which may be different from the levels needed for other processes

vacuoles

y
in a cell.

n
• Organelles with their contents c an be moved around within the cell.

O
• There is a larger area of membrane available for processes that happen

▴ Figure 6 Paramecium is a unicellular

i
within or across membranes.
eukaryote that feeds by endocytosis,

s
forming vacuoles in which ingested food is

Activity: Garlic cells and compartmentalization

r
digested. Aer formation of a vacuole, the

y
pH inside drops below pH2 and later rises
e
above pH7, to provide optimum conditions Garlic cells store a harmless sulfur-containing compound c alled alliin in their

p
for the seriesofenzymes that digest the vacuoles. They store an enzyme c alled alliinase in other parts of the cell.
v

food. This is only possible bec ause the

Alliinase converts alliin into a compound c alled allicin, which has a very strong

o
vacuole is a separate compartment. C an
smell and avour and is toxic to some herbivores. This reaction occurs when
i

you suggest two other advantages of food

herbivores bite into garlic and damage cells, mixing the enzyme and its
n

vacuoles as separatecompartments?

substrate. M any humans like the avour but to get it, garlic must be crushed

or cut, not used whole. You c an test this by smelling a whole garlic bulb, then
U

cutting or crushing it and smelling it again.

n
LHA

B2.2.4 Adaptations of the mitochondrion for

o
d

production of ATP by aerobic cell respiration

Mitochondria produce ATP by aerobic cell respiration. They are adapted to this
i
r

function by their structure.

t
o

• The outer membrane separates the contents of the mitochondrion from

a

the rest of the cell, creating a compartment specialized for the biochemic al
f

reactions of aerobic respiration.

u
x

• The inner mitochondrial membrane is the site of oxidative phosphorylation.

It contains electron transport chains and ATP synthase which together

l
O

generate a proton gradient and use it to produce ATP. Cristae are projections
a

of the inner membrane that increase the surface area available for oxidative

phosphorylation.
v

• The intermembrane space between the inner and outer membranes is where
E

a high concentration of protons is generated by the electron transport chains.

The volume of this space is very small, so a concentration gradient across the

inner membrane builds up rapidly.

• The matrix is the fluid filling the compartment inside the inner mitochondrial

membrane. It contains all the enzymes and substrates for the Krebs cycle

and the link reaction. By concentrating enzymes and substrates in the small

volume of the matrix, the reactions of these two parts of aerobic respiration

c an be performed more rapidly than if they were dispersed in the cytoplasm.

232
 Cells

LHA
outer mitochondrial membrane matrix

separates the contents of the mitochondrion contains enzymes of the

from the rest of the cell, creating a cellular Krebs cycle and link

compartment with ideal conditions for reaction

aerobic respiration
intermembrane

s
space into which

inner mitochondrial

protons are pumped

s
membrane

by the electron

contains electron

e
transport chain,

transport chains and

with a rapid

ATP synthase

r
concentration

buildup due to the

P
cristae are projections of the

y
small volume
inner membrane which increase

the surface area available for oxidative ribosomes and DNA

l
y
phosphorylation for expression of

n
t
▴

O
Figure 7 Electron micrograph of mitochondrion with annotated diagram of its structures

i
and their functions

s
r

y
Data-based questions: Structure and function in mitochondria
e

p
Study the electron micrographs in Figure 8 and then A One wall
v

answer the questions. B One membrane

o
C Two membranes
i

D One wall and one membrane

n

2. The mitochondrial matrix contains 70S ribosomes,

whereas the cytoplasm of eukaryotic cells contains

U

80S ribosomes. Which of these hypotheses is

n

consistent with this observation? [1]

i. Protein is synthesized in the mitochondrion.

o
d

ii. Ribosomes in mitochondria have evolved from

a) b)
ribosomes in bacteria.
i
r

iii. Ribosomes are produced by aerobic cell

t

respiration.
o

A (i) only
a

B (ii) only
f

C (i) and (ii)

x

D (i), (ii) and (iii)

l
O

3. Discuss the claim that the mitochondria in

a

c) d)
Figure 8b and Figure 8c are spheric al. [2]

▴ Figure 8 Electron micrographs of mitochondria: (a) from a

v

4. Predict, with reasons, which of the four types of

bean plant, (b) from c ardiac muscle, (c) from axolotl sperm,

mitochondria produces most ATP per unit time. [3]

(d) from batpancreas

E

5. Identify these other structures in the micrographs:

1. The uid-lled centre of the mitochondrion is c alled

a. to the right of the mitochondria in Figure 8a [1]

the matrix. What separates the matrix from the

b. to the right of the mitochondrion in Figure 8d. [1]

cytoplasm around the mitochondrion? [1]

233
 Form and function
LHA

B2.2.5 Adaptations of the chloroplast for

photosynthesis

Chloroplasts are quite variable in structure but share certain features:

s
• a double membrane forming the outer chloroplast envelope

• an extensive system of internal membranes c alled thylakoids, which are an

s
intense green colour due to chlorophyll

e
• small fluid-filled spaces inside the thylakoids

r
• a colourless fluid around the thylakoids c alled stroma that contains many

different enzymes.

y
In most chloroplasts there are stacks of thylakoids, c alled grana. If a chloroplast

l
has been photosynthesizing rapidly then there may be starch grains or lipid

y
droplets in the stroma.

n
thylakoid membranes stroma containing

O
70S ribsomes and

i
granum naked DNA

s
r

y
e

p
v

o
i
n

C
U

inner outer
n

membrane membrane

starch grain

chloroplast
lipid droplet
o
d

envelope
i
r

▴ Figure 9 Chloroplast structure

t
o

There is a clear relationship between the function of chloroplasts (described in

a

Topic C1.3) and their structure.

f

• Chloroplasts absorb light. Pigment molecules, arranged in photosystems

u

in the thylakoid membranes, c arry out light absorption. The large area of
x

thylakoid membranes ensures that the chloroplast has a large light-absorbing

l

c apacity. The thylakoids are often arranged in stacks c alled grana. Leaves
O

that are brightly illuminated typic ally have chloroplasts with deep grana

composed of many thylakoids, which allow more light to be absorbed.

v

• Chloroplasts produce ATP by photophosphorylation. A proton gradient

is needed. This develops between the inside and outside of the thylakoids.
E

The volume of fluid inside the thylakoids is very small, so when protons are

pumped in, a proton gradient develops after relatively few photons of light

have been absorbed. This allows ATP synthesis to begin.

234
 Cells

LHA
• Chloroplasts c arry out the many chemic al reactions of the C alvin cycle.

The stroma is a compartment of the plant cell in which the enzymes needed

for the C alvin cycle are kept together with their substrates and products.

This concentration of enzymes and substrates speeds up the whole C alvin

cycle. ATP and reduced NADP are needed for the C alvin cycle and are easily

s
available bec ause the thylakoids, where they are produced, are distributed

throughout the stroma.

s
e
one thylakoid

r
thylakoid

membrane

y
l
y

n
thylakoid

space

O
i
s
granum—a stack

of thylakoids

r
of thylakoids

y
▴ Figure 11 Drawing of part of the pea
e
chloroplast to show the arrangement of the

p
▴ Figure 10 Electron micrograph of pea chloroplast

thylakoid membranes
v

o
i

B2.2.6 Functional benets of the double

n

membrane of the nucleus

A general principle with phospholipid bilayers is that the hydrophobic core is

U

never exposed to water. If a membrane bec ame perforated by phospholipid

n

molecules moving apart, they would be drawn back together rapidly, closing the

perforation. Areas of membrane in water naturally adopt shapes such as spheres

o
d

or attered cisternae that avoid edges where the hydrophobic core is exposed.

Pores are formed using integral proteins, allowing specic molecules to pass
i
r

through, but larger holes through single membranes only occur when there has
t

been c atastrophic damage to a cell, for example when red blood cells burst aer
o

being bathed in pure water.

a
f

Proteins synthesized by ribosomes in the cytoplasm are needed in the nucleus to

u

form part of the structure of chromosomes. They also regulate gene expression
x

by promoting or repressing gene transcription. These proteins must be able to

l

enter from the cytoplasm. Messenger RNA, transfer RNA (tRNA) and ribosomes
O

produced in the nucleus are exported to the cytoplasm. The RNA molecules are

large, and ribosomes are even larger because they are assemblages of ribosomal
v

RNAs (rRNAs) and proteins. This means there is a need for unusually large pores

through the nuclear membrane—larger than the pores through channel proteins in
E

membranes. A double membrane is used to make a larger pore, with the inner and

outer membrane connected to form a circular hole. The rims of these nuclearpores

are lined with proteins that can control whether or not a protein passes through.

235
 Form and function
LHA

single-membraned
double-membraned

organelles such as vesicles,

organelles such as

vacuoles and lysosomes

chloroplasts

cisterna—a flattened

s
membrane sac such

as rough ER

s
e
double membrane

with pore, as in

r
nuclear membranes

y
l
y

n
▴ Figure 12 Membranes c an form a variety of shapes, but never begin or end

t
The double nuclear membrane has another functional benet. During both mitosis

O
and meiosis, the nuclear membrane breaks down to allow the chromosomes to be

i
moved to the poles of the cell. Nuclear membranes then reform around the new

s
groupings of chromosomes. This can easily be achieved with a double membrane.

r
Vesicles bud o, progressively breaking the whole nuclear membrane up into

y
vesicles, which are moved to the sides of the cell. Later, these vesicles can be used
e

p
to make new nuclear membranes by fusingtogether.
v

o
i

B2.2.7 Structure and function of free

n

ribosomes and of the rough endoplasmic

U

reticulum
n

▴ Figure 13 Freeze-etched electron

Ribosomes are large assemblages of rRNA and proteins. Eukaryote ribosomes

micrograph of the double nuclear

have a diameter of nearly 30nanometres. There are two subunits, one large

membranes, with nuclear pores visible and

o
d

and one small. The small subunit has a binding site for mRNA. The large subunit

vesicles in the surrounding cytoplasm

has three binding sites for tRNA molecules, an area that c atalyses the formation
i

of peptide bonds and an exit tunnel for the synthesized polypeptide. Protein
r

synthesis by ribosomes is described in Topic D1.2.

t
o

Ribosomes that are not attached to membranes in the cytoplasm are known

as free ribosomes. Polypeptides synthesized by them are released into the

f

cytoplasm and either remain there or enter the nucleus. The cytoplasm of a
x

typic al cell contains a wide range of proteins, some c arrying out housekeeping
l

roles, for example enzymes that c atalyse glycolysis, and others performing the
O

specialized functions of the cell.

If a ribosome synthesizes a polypeptide that must be transported to a specic

v

loc ation, the ribosome becomes attached to the rough endoplasmic reticulum.

This organelle consists of cisternae, which are attened sacs bounded by a

E

single membrane. The polypeptide passes into the lumen of the rER and is then

transported elsewhere in the cell by a vesicle that buds o from the rER. The usual

initial destination for these polypeptides is the Golgi apparatus, with many of

them ultimately secreted from the cell.

236
 Cells

LHA
proteins synthesized by free

ribosomes are released into the

cytoplasm and remain there, or they

enter the nucleus, or are absorbed

by chloroplasts or mitochondria

s
proteins synthesized by

s
ribosomes on the rER pass into

the cisterna of the ER via a

e
translocaton channel and

remain there or are transported

r
elsewhere in vesicles

vesicles transport

P
proteins to lysosomes,

y
mRNA 5’ ’
the Golgi apparatus or
mRNA 5’ ’

l
the plasma membrane

n
t

O
i
s
lumen of

r
endoplasmic

y
reticulum
e

p
v

protein vesicles bud

o
off from the rER
i
n

C
U

▴ Figure 14
o
d

Applying technology
i
r

t
o

The protein data bank (PDB) is a public database

a

containing data regarding the three-dimensional structure

f

for many biologic al molecules. In 2000, structural

u

biologists Venkatraman R amakrishnan, Thomas A. Steitz

x

and Ada E. Yonath made the rst data about ribosome

l

subunits available through the PDB. In 2009, they

O

received a Nobel Prize for their work on the structure of

ribosomes. Visit the RCSB protein data bank to obtain

v

images of the Thermus thermophilus ribosome. Use the

search function to loc ate image 1jgo. Using the structure

E

view, rotate the image to visualize the small subunit and

the large subunit, the associated tRNA molecules and

mRNA molecules.

▴ Figure 15 Molecular visualization of a functioning ribosome.

Key: mRNA yellow; tRNAs pink, purple and blue; rRNA white in

the small subunit and grey in the large subunit; proteins violet in

the small subunit and red in the large subunit

237
 Form and function
LHA

B2.2.8 Structure and function of the

Golgiapparatus

The Golgi apparatus is a stack of attened sacs (cisternae) in which polypeptides

made by the rough endoplasmic reticulum are processed. The polypeptides are

s
transported from the rER in vesicles. Enzymes inside the cisternae c an change the

s
polypeptide in numerous ways—for example, by adding c arbohydrate to make

glycoprotein or by adding phosphate or sulfate groups. The quaternary structure

e
of proteins c an be established by assembling polypeptides and other subunits.

r
When the processing of a protein is completed, it is transported from the Golgi

P
apparatus to its destination in a vesicle. This may be a lysosome or a food vacuole

y
formed by endocytosis. For proteins that are being secreted, the

destination is the plasma membrane of the cell. For example, digestive

l
enzymes are secreted by pancreas cells when vesicles move from to

n
TRANS
the plasma membrane and fuse with it to release the enzymes from
CIS

SIDE

t
SIDE thecell.

O
i
Processing proteins in the Golgi apparatus is sequential, with each

s
vesicles
protein gradually moving through the cisternae from the side nearest

bringing

the rER (the cis side) to the opposite side (the trans side). Two models

r
polypeptides

y
vesicles have been proposed to explain how proteins could move through the
from the

carrying
e
rER Golgi apparatus.

p
processed

• The vesicle transport model in which the cisternae do not move

proteins to the
v

plasma and vesicles transfer proteins between them.

o
membrane for

• The cisternal maturation model in which vesicles from the

i

secretion

rER coalesce to form new cisternae on the cis side, which then
n

gradually move through the Golgi until they reach the trans side,

cisternae

where they break up intovesicles.

U

Currently, evidence for the cisternal maturation model is stronger, but

▴ Figure 16 According to the cisternal maturation

many questions remain about the functioning of the Golgi apparatus,

model, cisternae are formed on the cis side from

coalescing vesicles and the move through the stack. including the reason for the cisternae needing to be kept together in a
o
d

When they reach the trans side they fragment into vesicles stack.
i
r

t
o

B2.2.9 Structure and function of vesicles

a

incells
f

u
x

Vesicles are rounded sacs made of a single layer of membrane, and the material

inside it. They are typically small and dynamic structures that are continuously
l
O

made, moved and merged within cells. They are made by pinching o a small area of
a

membrane from a larger area. This happens in endocytosis in order to take in a small

droplet of uid from outside the cell. The protein clathrin helps with thisprocess.
v

Clathrin is a three-legged protein (Figure 17) that becomes positioned on the

E

inner face of the plasma membrane when a vesicle is being made. Adjacent

clathrin molecules bind to each other to form a lattice of pentagons and/or

hexagons. This process helps the plasma membrane to become indented and

eventually to detach to form a sphere of membrane with a clathrin c age around it.

238
 Cells

LHA
s
s
e
r
P

y
l
y

n
▴ Figure 17 Three-legged clathrin molecules bind

to each other forming a c age to support a vesicle

O
Vesicles c an be used to move materials around inside cells. There are two general

i
reasons for this.

s
• In some c ases, it is the contents of the vesicle that need to be moved. The

y
transport of neurotransmitters to the presynaptic membrane of a neuron is an

example of moving materials in vesicles.

e

p
• In other c ases, it is the membrane of the vesicle or the proteins in the
v

membrane that are the reason for vesicle movement. In a growing cell,

o
the area of the plasma membrane needs to increase. Phospholipids are
i

synthesized next to the rER and become inserted into the rER membrane.
n

Ribosomes on the rER synthesize membrane proteins which also become

inserted into the membrane. Vesicles bud off the rER and move to the

plasma membrane. They fuse with it, each increasing the area of the plasma
U

membrane by a very small amount. This method c an also be used to increase

n

the size of organelles in the cytoplasm such as lysosomes and mitochondria.

o
d

Linking questions
i
r

1. What are examples of structure–function correlations at each level of

o

biologic al organization?
a
f

a. Outline the relationship between the structure and function of

u

glycoproteins and glycolipids. (B2.1.9)

x

b. Explain the role of the Golgi apparatus in processing and secretion of

l
O

protein. (B2.2.8)
a

c. Draw the anatomy of the female reproductive system and annotate

v

the structures with their functions. (D3.1.4)

2. What separation techniques are used by biologists?

E

a. Outline the technique of gel electrophoresis. (D1.1.5)

b. Discuss the relationship between the denition of organelles and the

techniques of cellular fractionation and ultracentrifugation. (B2.2.1)

c. Explain the separation and identic ation of photosynthetic pigments

by chromatography. (C1.3.4)

239
 B2.3 Cell specialization

What are the roles of stem cells in multicellular organisms?

s
s
Some lizards esc ape from a predator by shedding their tail. In

the weeks that follow, a tail c an regrow. When the gecko’s tail

e
regrows, it has skin, muscle and nerve bres, but the lost vertebrae

r
are not replaced. Why does this happen? If a person loses a nger

in an accident, why does the nger not re-grow? An early embryo

y
divides repeatedly. Up to the eight-cell stage, the cells c an be

separated and still give rise to an entire organism. Gradually they

l
become more restricted in their potential to become all cell types.

y
▴ Figure 1 Gecko that has lost its tail

n
What role do stem cells play in these examples?

O
How are dierentiated cells adapted to their specialized functions?

i
s
Figure 2 shows the ultrastructure of a hepatocyte while Figure 3 shows the ultrastructure of several neurons. What is

r
the identity of the red dots in the nerve cell? C an you deduce which is the pre-synaptic cell and which is the post-

y
synaptic cell? What are the blue organelles? How does the structure of the neuron dier from the hepatocyte? How
e
are the structures of the organelles related to their functions? What do neurons and hepatocytes have in common?

p
v

o
i
n

C
U

n
o
d

i
r

t
o

a
f

u
x

l
O

▴ Figure 2 Liver cells ▴ Figure 3 Cells in the cerebellum of the brain

a

SL and HL AHL only

v

B2.3.1 Production of unspecialized cells following fertilization and B2.3.7 Adaptations to increase surface area-to-
E

their development into specialized cells by dierentiation volume ratios of cells

B2.3.2 Properties of stem cells B2.3.8 Adaptations of type I and type II

B2.3.3 Loc ation and function of stem cell niches in adult humans pneumocytes in alveoli

B2.3.4 Dierences between totipotent, pluripotent and B2.3.9 Adaptations of c ardiac muscle cells and

multipotent stem cells striated muscle bres

B2.3.5 Cell size as an aspect of specialization B2.3.10 Adaptations of sperm and egg cells

B2.3.6 Surface area-to-volume ratios and constraints on cell size

240
 Cells

B2.3.1 Production of unspecialized cells

following fertilization and their development

into specialized cells by dierentiation

s
Fertilization is the fusion of a male and female gamete to produce a single cell.

In multicellular organisms, this cell divides repeatedly to generate an embryo of

s
many cells. Mitosis ensures that the cells in an embryo are all genetic ally identic al.

e
They have all the genes in the organism’s genome and could develop in any way.

r
In an early-stage embryo, the cells are unspecialized. As an embryo grows, its

cells develop along dierent pathways and become specialized for specic

y
functions. This allows each cell to c arry out its function more eciently than if it

had multiple roles. The cell c an develop the ideal structure, with the enzymes

l
needed to c arry out all the chemic al reactions associated with its function. The

n
development of cells in dierent ways to c arry out specic functions is c alled

dierentiation. In humans, there are 220 distinctively dierent highly specialized

t
cell types, all of which develop by dierentiation.

O
i
When a gene is being used in a cell, we say that the gene is being expressed. In

s
simple terms, the gene is switched on and the information in it is used to make

r
a protein or other gene product. The development of a cell involves switching

y
on and expressing particular genes but not others. Cell dierentiation happens
e
bec ause a dierent sequence of genes is expressed in dierent cell types.

p
v

▴ Figure 4 In this Drosophila embryo,

In a multicellular organism, there must be enough cells of each type and they

o
a uorescent marker shows cells that are

must all be in the positions within the body where they are needed. The position
i

expressing the genes for the two proteins

of a cell in the embryo must therefore determine how it dierentiates. Gradients

AbdA and Exd. These proteins form a

n

of signalling chemic als indic ate a cell’s position in the embryo and determine

complex that binds to DNA to regulate

which pathway of dierentiation it follows. These chemic als are regulators of

expression of specic genes. The marker

U

gene expression. For example, gradients of retinoic acid guide dierentiation of

shows that this is happening in some

cells in the development of forelimbs, pancreas, lungs, kidneys and other organs.
n

segments of the embryo but not others

o
d

B2.3.2 Properties of stem cells

i
r

In the 19th century, the term “stem cell” was given to the zygote and the cells
t

of the early embryo bec ause all the tissues of the adult stem from them. Stem
o

cells have been intensively researched bec ause of their role in development and

bec ause they have many potential therapeutic or regenerative uses.

f

u
x

A stem cell c an divide repeatedly. In theory, there is no limit to the number

of times it c an split into two cells. Stem cells in the skin divide repeatedly
l
O

throughout our lives, allowing us to replace lost skin cells. Stem cells in the testes
a

also divide endlessly. This is the rst stage of gamete production and allows males

to produce vast numbers of sperm throughout adulthood.

v

Cells produced by division of a stem cell might remain as stem cells or

E

dierentiate into a specic cell type. If they dierentiate, they are no longer stem

cells. A stem cell is either undierentiated or partially dierentiated; they are

always c apable of dierentiating along dierent pathways.

241
 Form and function

s
s
e
r
P

y
l
phloem
xylem layer of stem

n
cells (cambium)

t
▴ Figure 5 Tree trunks have a cylinder of stem cells on the inner side of their bark. Unlike the layer of stem cells in human skin which

O
i
produces cells on one side, the layer of stem cells in the trunk generates cells on both sides. On the inner side, the new cells dierentiate

into xylem; on the outer side, they become phloem. Xylem and phloem are both used for transport but they transport dierent substances

s
by dierent methods. For this reason, they are dissimilar in structure. Xylem tissue is the wood that supports the tree. Bec ause thestem cells

r
in the bark divide endlessly, more xylem is added to the trunk every year and itcontinues to widen throughout the tree’s life. That may be

y
thousands of years in long-livedtrees
e

p
v

o
B2.3.3 Loc ation and function of stem cell
i

niches in adult humans

n

Some stem cells remain in the adult body. They are present in many human

tissues, including bone marrow, skin and liver. Stem cells give these tissues
U

considerable powers of regeneration and repair. The precise loc ation of

n

stem cells within a tissue is c alled the stem cell niche. It must provide a

microenvironment with conditions needed for the stem cells to remain inactive
o
d

and undierentiated over long periods of time, and also for them to proliferate

rapidly and dierentiate when required.

i
r

In striated (skeletal) muscle, there are stem cells that remain inactive unless
t
o

there is muscle injury. Changes in the stem cell niche then c ause these cells
a

to proliferate and dierentiate, to replace damaged muscle tissue. Striated

f

muscle is highly regenerative aer damage. Bone marrow and hair follicles
u

are two examples of stem cell niches where the microenvironment promotes
x

continuous stem cell proliferation and dierentiation. This results in production of

l

replacement blood cells and in hair growth.

O

Stem cell niches are of research interest bec ause if they c an be simulated outside
v

the body for a particular stem cell type, it should be possible to generate human

tissue in vitro (literally, in glass; that is, in the laboratory) and use it in restorative
E

surgery. There are also non-therapeutic uses for stem cells if appropriate

microenvironments c an be created. One possibility is to use them to produce

large quantities of striated muscle bres (that is, meat) for human consumption.

The beef burgers of the future may therefore be produced from stem cells,

without the need to rear and slaughter c attle.

242
 Cells

Data-based questions: Adaptations of the Western spadefoot toad

The Western spadefoot toad (Scaphiopus hammondii) lives in desert areas in C alifornia and lays its eggs in pools formed

by rain. When the egg rst hatches, its body form is referred to as the tadpole stage. At some point, it undergoes

s
metamorphosis (a change in body form) to develop into the adult toad. If the pool where the eggs have been laid

shrinks due to a lack of rain, the tadpoles quickly develop into small adult toads. If there is sucient rain and the pool

s
persists, the tadpoles develop more slowly and grow large before developing into adult toads.

e
1. Suggest how undergoing metamorphosis at dierent times in response to high and low water levels helps

thesurvival of the toad. [3]

r
An experiment was c arried out to determine what hormones might be involved in triggering development in response

P
to pond drying. Tadpoles were raised in a constant high-water environment. They were then divided into two groups.

y
3

One group was transferred to a tank containing 10 dm of water — a high-water environment. The other group was

l
transferred to a tank of the same size containing only 1 dm of water — a low-water environment. The concentrations of

y
thyroxine and corticosterone were measured in each group. The results are shown in Figure6.

n
/ noitartnecnoc

2. Compare and contrast the

t
/ noitartnecnoc

O
concentrations of thyroxine

i
60 4
ssam

ssam

and corticosterone in the

s
two groups. [2]
3
yd ob

yd ob

40

r
3. Suggest how cellular

y
2
enoretsocitroc
1–

1–

dierentiation plays a role

enixoryht

20
e
g gn

g gn

1
in metamorphosis in the

p
spadefoot toad. [2]
v

0 0

high-water low-water high-water low-water

o
environment environment environment environment
i
n

▴ Figure 6
U

B2.3.4 Dierences between totipotent,

o

pluripotent and multipotent stem cells

d

E arly-stage embryos are entirely composed of stem cells. These cells are
i
r

totipotent. This means that they c an dierentiate into any cell type. Totipotent
t

embryonic stem cells are potentially very useful, for example, in the growth of
o

whole replacement hearts, kidneys or other organs.

f

Cells gradually commit to particular pathways of dierentiation during embryo

u
x

development. This involves a series of points at which a cell commits to develop

along one pathway or another. Embryonic stem cells change from being
l
O

totipotent to pluripotent. A pluripotent cell is still c apable of dierentiating into a

a

range of cell types, but not every cell type.

v

The stem cells that remain in the adult body are more restricted in potential, but if

they c an dierentiate into several types of mature cell, they are considered to be
E

multipotent. Haematopoietic stem cells in bone marrow are multipotent bec ause

they c an generate dierent types of blood cell, but not other cell types.

243
 Form and function

ATL Social skills: Actively seeking and considering the perspective of others

When considering debatable represent the inner cell mass, the part of the embryo that

questions, individuals bring will become the foetus. It is these cells that are used in

s
dierent perspectives to the stem cell therapies.

conversation. To be open-minded

1. Both skin cells and embryos c an be cultured in vitro.

s
means that you recognize that

Do they have the same ethic al status or should

your own view does not exhaust

e
there be a dierence in the rules that govern their

the possibilities. It also requires a

use? Would an accident c ausing the destruction of

▴ Figure 7

r
genuine curiosity regarding other

embryos be of equal concern to an accident c ausing

possibilities and a willingness to suspend judgement until

the destruction of a culture of epidermal cells?

y
all the facts have been considered.

2. Hyperovulation c an be medic ally induced to increase

Embryonic stem cells are totipotent and have unique

l
the production of eggs in women to be used in the
properties that make them valuable tools for therapy

n
creation of embryos. What concerns, if any, arise from
and medic al treatments. Figure 7 shows a diagram of

compensating women for egg donation?

a blastocyst, the uid-lled ball of cells that forms aer

t
several divisions of a fertilized egg. The orange cells

O
i
s
r

y
B2.3.5 Cell size as an aspect of
e

p
specialization
v

The size of a mature dierentiated cell is one way in which it is adapted to perform

o
its function. Evidence for this in humans is provided by the examples inTable 1.
i
n

Cell type Adaptation to function by cell size

sperm 50 µm long, which is longer than most cells but sperm are
U

extremely narrow so they have one of the smallest volumes

n

of any human cell. Narrowness and small volume reduce

resistance and allow sperm to swim to the egg more easily.

o
d

egg 110 µm in diameter and spherical in shape, so egg cells have the

largest volume of any human cell. This allows large quantities of

i
r

food reserves to be stored in the cytoplasm. In birds, egg cells

t
o

are even larger, with huge amounts of stored food (yolk).

a

red blood 6 µm to 8 µm in diameter but indented on both sides and only

f

cells about 1 µm thick in the middle. The small size and shape allow
u
x

passage along narrow c apillaries and gives a large surface area-

to-volume ratio, so loading and unloading of oxygen is faster.

l
O

white blood B-lymphocytes are only about 10 µm in diameter when inactive

a

cells but enlarge to as much as 30 µm if they are activated and

v

become antibody-secreting plasma cells. The extra volume is

cytoplasm with rER and Golgi apparatuses for protein synthesis.

E

cerebellar The cell body is only 4.0 µm in diameter, but twin axons extend

granule cells for about 3 mm (3,000 µm) in the cerebellar cortex. The very

small volume of these neurons allows the cerebellum to

accommodate 50 billion of them — 75% of the brain’s neurons.

244
 Cells

motor The cell body is about 20 µm in diameter. This large size allows

neurons enough proteins to be synthesized to maintain the immensely

long axon. It can extend for a metre or more (a million µm), so can

carry signals from the central nervous system to a distant muscle.

◂ Table 1 Cell sizes

s
striated Striated muscle bres are larger than normal cells, with a

muscle bres diameter of 20 µm to 100 µm and lengths that c an exceed

s
100 mm (100,000 µm). These dimensions allow the bre to

e
exert greater force and contract by a greater length than

smaller muscle cells.

r
cerebellar

y
granule cell

5 μm

l
red blood
◂ Figure 8 Human cells

n
cell
vary widely in diameter and

8 μm
even more widely in volume

O
inactive

i
B-lymphocyte

s
striated human egg
motor neuron
10 μm antibody-secreting

muscle fibre cell 100 μm

cell body
plasma cell

r
100 μm

y
25 μm
30 μm
e

p
B2.3.6 Surface area-to-volume ratios and
Activity:
v

constraints on cell size

o Effect of size on surface

i

M any chemic al reactions take place in the cytoplasm of cells. These reactions

area-to-volumeratio
n

are known collectively as the metabolism of the cell. The rate of these reactions

C alculate the volume and surface

(the metabolic rate of the cell) is proportional to the volume of the cell. For

area and then the surface area-to-

U

metabolism to continue, substances used in the reactions must be absorbed by

volume ratio of cubes with sides

n

the cell and waste products must be removed. Substances move into and out of

1 mm, 10 mm and 100 mm. What is

cells through the plasma membrane at the surface of the cell. The rate at which

the trend?
substances cross this membrane depends on its surface area.
o
d

The relative amounts of surface area and volume c an be expressed

i

mathematic ally as a ratio:

r

surface area (mm )

t

surface area-to-volume ratio =

o

volume (mm )
a

same cube

Surface area-to-volume ratio is very important to a cell. If it is too small, substances

f

unfolded
u

will not enter the cell as quickly as they are required. Also waste products will
x

accumulate bec ause they are produced more rapidly than they c an be excreted.

Surface area-to-volume ratio is also important in relation to heat production ▴ Figure 9

l
O

and loss. If the ratio is too small, cells may overheat bec ause the metabolism
a

produces heat faster than it is lost over the cell’s surface.

v

Mathematic al models: Surface area-to-volume ratio

E

Models are simplied versions of complex systems. The eect of size on the

surface area-to-volume ratio of cells c an be modelled using cubes with sides of

dierent lengths. Although the cubes have a simpler shape than real organisms,

sc ale factors operate in the same way, so the trend for the cubes will also

operate in cells of more rounded or irregular shape, as long as the shape stays

the same as the dimensions increase.

245
 Form and function
LHA

B2.3.7 Adaptations to increase surface

area-to-volume ratios of cells

Some cells are specialized for exchange processes. Examples are proximal

convoluted tubule cells in the kidney that reabsorb useful substances from

s
glomerular ltrate, and red blood cells (erythrocytes) which transport oxygen

s
from the lungs to respiring tissues. These cells must be able to transport

substances rapidly in and out across their plasma membrane. They all show

e
adaptations that increase their surface area-to-volume ratio.

r
Red blood cells

y
The shape and small size of red blood cells gives them a large surface area-to-

volume ratio, which helps them load and unload millions of oxygen molecules

l
rapidly. They are only about 8 µm in diameter and their biconc ave disc shape

n
gives them a lower volume than a sphere of the same diameter and a smaller

▴ Figure 10 Red and white blood cells maximum distance from any part of the cytoplasm to the plasma membrane.

O
Proximal convoluted tubule cells

i
Near the outer surface of the kidney there are large numbers of narrow, coiled

s
tubes, c alled proximal convoluted tubules. These tubules receive the large

y
volumes of uid that are ltered out of the blood in the kidney. They reabsorb

most of this ltrate, including all molecules of useful substances such as glucose.
e

p
The wall of the proximal convoluted tubules is only one cell thick, with the inner
v

apic al membrane in contact with the ltrate and the outer basal membrane

o
close to blood c apillaries. To be reabsorbed from the ltrate to the blood, a
i

molecule or ion must pass through both the apic al membrane and the basal

membrane. Channel proteins and pump proteins in these membranes ensure

n

that only substances required by the body are reabsorbed, with waste products

such as urea remaining in the ltrate. The apic al membrane has large numbers of
U

microvilli, which provide a large surface area. The basal membrane has infoldings
n

(invaginations), which also increase the surface area. Both the apic al and basal

membranes therefore have ample space for the channel and pump proteins that
o
d

c arry out selective reabsorption.

i
r

B2.3.8 Adaptations of type I and type II

o

pneumocytes in alveoli
f

The lungs contain huge numbers of alveoli. These air sacs provide a very large
x

total surface area for diusion. The wall of the alveolus is one cell thick and is an
l

epithelium. There are two types of cell in the alveolar epithelium.

O

• Type I pneumocytes (AT1 cells) are adapted for diffusion of oxygen

and c arbon dioxide. This is a passive process, so there is little need for
v

mitochondria or other organelles and the volume of cytoplasm is small.

These are very wide but extremely thin cells. The thickness is only about
E

0.15 μm, widening slightly where the nucleus is loc ated. The wall of the

adjacent c apillaries also consists of a single layer of very thin cells. The air

in the alveolus and the blood in the alveolar c apillaries are less than 0.5 μm

apart. The distance over which oxygen and c arbon dioxide must diffuse is

thus very small, increasing the rate of gas exchange.

246
 Cells

LHA
• Type II pneumocytes (AT2 cells) are more numerous than type I cells (they

represent 90% of alveolar cells) but they occupy only about 5% of the

alveolar surface area. They are about 10 µm across with a dense cytoplasm

containing mitochondria, rough endoplasmic reticulum and lysosomes.

L arge amounts of phospholipid are synthesized in the cytoplasm and stored

s
in lamellar bodies, which are vesicles containing many layers of phospholipid

and some proteins. The contents of the lamellar bodies are secreted

s
byexocytosis.

e
lateral membrane microvilli providing

r
separating the cell from an a large surface area

adjacent cell in the tubule wall of apical membrane

y
l
y

n
many mitochondria

10 μm
to provide ATP for

t
active transport

O
i
s
r

y
basement lamina—a porous layer of infoldings providing a

glycoproteins that strengthens the large surface area of

e

p
single layer of cells in the wall basal membrane
v

▴ Figure 11 Proximal convoluted cell with microvilli and invaginations

o
i

The alveolus is lined by a lm of moisture, which allows oxygen in the alveolus to
type I pneumocyte
n

dissolve and then diuse to the blood in the alveolar c apillaries. It also provides

cell nucleus
an area from which c arbon dioxide c an pass into the air and be exhaled.
U

Phospholipids secreted by the lamellar bodies spread to form a single layer of

basement lamina

molecules on the outer surface of the lm of moisture, with the hydrophilic heads
n

of the phospholipids inwards and the hydrophobic tails facing outwards to the air
endothelium of capillary

in the alveolus. Proteins secreted from the lamellar bodies are dispersed between

air in alveolus
o
d

the phospholipid molecules. The layer of phospholipids and proteins acts as

blood plasma

a surfactant, reducing surface tension. Without surfactant, the alveolus might

i

red blood cell

r

collapse on itself with the sides adhering due to hydrogen bonding between
t

water molecules.
o

1 μm
a
f

▴ Figure 12 Flattened cells in the walls of

u

the alveolus and blood c apillary

x

l
O

a
v
E

◂ Figure 13 Type II pneumocyte with a

prominent nucleus (blue). The cytoplasm

contains many organelles including lamellar

bodies (brown). L ayers of phospholipid are

visible in the lamellar bodies. The irregular

surface of the cell is due to recent exocytosis

247
 Form and function
LHA

B2.3.9 Adaptations of c ardiac muscle cells

and striated muscle bres

Muscle tissue is contractile — it c an shorten in length. When it does this it exerts a

pulling force that c an be used to c ause movement. To return to its original length,

s
a pulling force must be exerted on the muscle. This is usually provided by another

s
muscle, so many muscles work in antagonistic pairs — the contraction of one

c auses the lengthening of the other.

e
The muscles that are used to move the body are attached to bones, so they are

r
c alled skeletal muscles. When their structure is viewed using a light microscope,

P
stripes are visible. Bec ause of this, they also c alled striated muscle. Striated

y
muscle is composed of many long, unbranched cylindric al structures known

as muscle bres, which are arranged in parallel. Although a single plasma

l
membrane surrounds each muscle bre, there are many nuclei present and

n
muscle bres are much longer than typic al cells. These features are bec ause

t
embryonic muscle cells fuse together to form muscle bres.

O
i
Electron microscopes reveal that within each muscle bre there are many parallel,

s
cylindric al structures c alled myobrils. These have alternating light and dark

▴ Figure 14 Light micrograph of striated

bands. In the centre of each light band is a disc-shaped structure, referred to as

y
muscle bres with stripes and multiple
the Z-line. Muscle contraction is explained in Topic B3.3

nuclei visible
e

p
one sarcomere
v

o
i
n

C
U

light band Z-line dark band

n

▴ Figure 15 Structure of a myobril

o
d

▸ Figure 16 Part of one striated muscle

bre is visible in this electron micrograph,

i
r

with mitochondria between the myobrils

t

coloured blue. Light bands (green) and dark

o

bands (red) are aligned in all the myobrils

a

within the muscle bre. It is this that gives

f

the striatedappearance
u
x

C ardiac muscle forms the wall of the heart. As in skeletal muscle, there are

myobrils, with the light and dark bands aligned, so c ardiac muscle has a striated
l
O

appearance. However, unlike the elongated bres of skeletal muscle, c ardiac

a

muscle is composed of much shorter cells, most of which only have one nucleus.

Where the end of one cell contacts the end of another cell, there is a specialized
v

junction c alled an interc alated disc. C ardiac muscle cells are branched, so

interc alated discs connect each cell at both ends with several other cells. In an
E

interc alated disc, there are connections between the plasma membranes and

cytoplasm of adjacent c ardiac muscle cells, allowing electric al signals to be

propagated rapidly from cell to cell. If one c ardiac muscle cell in the wall of the

heart is stimulated to contract, the stimulus is passed on to all the other cells, so

there is a synchronization of muscle contraction and blood is pumped quickly out

of the heart.

248
 Cells

LHA
◂ Figure 17 Light micrograph of c ardiac

muscle tissue with short, branched cells and

striations (pink). Interc alated discs (purple)

are clearly visible where cells meet. E ach

cell contains a single nucleus (purple)

s
s
e
r
P

y
l
y

n
t

O
i
Whether or not a muscle bre should be classed as a cell is debatable. They are

s
enclosed in a plasma membrane, but have many nuclei, rather than just one.

r
They are much larger than most animal cells, with an average length in humans of

y
about 30 mm, whereas other human cells are mostly less than 0.03 mm in length.
e

p
v

o
B2.3.10 Adaptations of sperm and egg cells
i

Egg cells and sperm cells are gametes each containing a haploid nucleus that
n

passes on genes from parent to ospring. Beyond these similarities, male and

female gametes in humans are radic ally dierent. Sperm move actively and
U

rapidly whereas egg cells are moved passively and relatively slowly. Egg cells
n

have food reserves needed for embryo development whereas sperm have little

or no stored food.
o
d

Egg cells have structures that enable them to receive one sperm (and no more) in

the process known as fertilization.

i
r

• Zona pellucida — a layer of glycoproteins containing ZP3 to which sperm

t

bind and which a sperm c an penetrate, but which later c an be chemic ally
o

altered to prevent any more sperm from penetrating.

f

• Binding proteins in the plasma membrane which help it to fuse with the
u

membrane of the sperm, allowing the sperm nucleus to enter the egg.
x

• Cortic al granules — vesicles of enzymes near the plasma membrane of the

l
O

egg cell which are released into the zona pellucida and make it impenetrable
a

after the nucleus of a sperm has entered the egg.

v

Egg cells also have structures which provide the resources needed for the zygote

and then the embryo to develop.

E

• Yolk — this is the large volume of cytoplasm inside the egg cell that contains

stores of lipids and other foods.

• Mitochondria — these produce ATP and divide repeatedly to generate all the

mitochondria in an adult’s body.

• Centrioles — these are needed for mitosis.

249
 Form and function
LHA

haploid

nucleus

cytoplasm (or yolk)

two centrioles containing droplets of fat

s
first polar cell

s
e
r
diameter of egg

cell = 110 µm

y
l
y

n
t
plasma

O
membrane

i
cortical granules

s
layer of follicle cells

r
layer of gel composed

y
(corona radiata)
of glycoproteins
e
(zona pellucida)
▸ Figure 18 Structure of a human egg cell

p
v

Sperm cells are adapted to transfer a haploid nucleus from the testis of a male

to the cytoplasm of an egg cell in the

o
oviduct of a female. This is a competitive
i

process — the rst sperm to reach and penetrate an egg cell is the only one to
n

achieve its role. Sperm cells have structures which allow them to swim rapidly.

• Tail — a very long flagellum with the characteristic arrangement of 9 + 2

U

microtubules that generates the force needed for forward motion with its
n

beating action.

• Midpiece with mitochondria — multiple mitochondria are wound round

o
d

the microtubules at the base of the tail, where they c an supply the large

quantities of ATP needed for the motion of the tail.

i
r

• Head — streamlined in shape and very narrow due to the nucleus having
t
o

tightly packed chromosomes and the volume of cytoplasm being very small,
a

so resistance to movement is minimized.

f

Sperm also have structures that they use to insert their nucleus into the eggcell.
u
x

• Receptors in the plasma membrane for ZP3 glycoproteins in the zona

pellucida to which the sperm binds.

l
O

• Acrosome — a sac of enzymes that digest proteins and polysaccharides in the

protective zona pellucida so the sperm c an reach the plasma membrane of

v

the egg cell.

• Binding proteins in the inner acrosomal membrane, revealed after exocytosis

E

of the acrosome, which bind to proteins in the plasma membrane of the egg

cell, leading to fusion of the membranes and entry of the sperm nucleus to

the egg.

250
 Cells

LHA
haploid nucleus

acrosome

mid-piece tail (40 µm long, two-thirds of

(7 µm long) it omitted from this drawing)

head (1. μm

thic,  μm wide

s
and 4 μm long)

microtubules in a

s
centriole

9+2 arrangement

e
plasma membrane
helical protein fibres to

mitochondria strengthen the tail

r
▴ Figure 19 Structure of a human sperm cell

y
l
Linking questions

n
1. What are the advantages of small size and large size in biological systems?

O
a. Explain the dierences in the size of cells in three dierent kingdoms.

i
(A2.2.8)

s
b. Explain the challenges associated with gas exchange as cells

y
become larger. (B3.1.1)
e
c. O utline the factors that lead to variation in the speed of nerve

p
impulses. (C2.2.4)
v

2. How do cells become dierentiated?

o
i

a. Outline the role of methylation and acetylation in gene expression.

n

(A2.2.13)

b. Distinguish between totipotent, pluripotent and multipotent cells.

U

(B2.3.4)
n

c. Discuss the process of cellular dierentiation with respect to the

process of spermatogenesis. (D3.1.4)

o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

251
 Form and function

TOK

Should some knowledge not be sought

s
s
on ethic al grounds?

e
Ethics is the ac ademic study that looks into questions of

right and wrong. Scientists are sometimes confronted

r
with situations where their investigations raise ethic al

y
questions. For example, they might want to explore a topic

using methods that some people consider wrong or the

l
investigation itself might result in an outcome that some

n
people consider wrong.

t
There are many scientic activities from the 20th century

O
Figure 1 Henrietta L acks

involving human subjects in experiments that should

i
standing outside her home several

not have been c arried out on ethic al grounds. These

s
years before her death from

experiments include:

cervic al c ancer at the age of 31

r
• exposure of humans to debilitating diseases (the

y
had no success growing c ancer cells in the laboratory. HeL a
Tuskegee Syphilis experiment)
e
cells, however, thrived. In the 70years since 1952, HeL a

p
• deliberate exposure of humans to radiation

cells have been used in research around the world.

v

• surgic al experiments

o
The Tuskegee Syphilis Study was c arried out from 1932
• tests with mind-altering substances.
i

to 1972 by the United States Public Health Service. The

n

Some of the most famous examples of previous unethic al objective of the study was to discern the natural course

research practices would be unlikely to happen today of untreated syphilis in black men. Of the 600male

bec ause of the existence of institutional review boards participants, about 400 had syphilis. There was none of
U

(IRBs). An IRB is a committee within a university or research the transparency needed to ensure informed consent
n

organization that reviews research proposals to ensure and the men were never given the option of leaving the

they follow the ethic al principles necessary to protect study. Participants were not told their diagnosis and were
o
d

human subjects. An IRB has the authority to approve, reject only treated with placebos, although during the study

or require modic ations to research proposals within the it bec amewell known that penicillin was an eective
i
r

institution in which it operates. treatment for syphilis.

t
o

Henrietta L acks was a patient at Johns Hopkins University in Based on the lack of opportunity to get treatment when
a

the early 1950s. She had a c ancerous cervic al tumour that available, the Tuskegee study was “ethic ally unjustied”.
f

ultimately led to her death. A sample of her c ancer cells Of the original participants, 28 died as a result of syphilis
u

taken during the course of her medic al treatment was sent and a further 100 died of complic ations of the disease.
x

to a tissue lab. It was discovered in the laboratory that the Forty wives were infected and 19 children were born with
l

cells survived and were able to multiply in vitro. The cells congenital syphilis.
O

were nicknamed HeL a cells. HeL a cells have been highly

In modern experiments, if a treatment is found to be more

useful for studying a range of phenomena, though they
v

eective than the placebo, a study is typic ally stopped and

were used for this purpose without her permission. While

access to the successful treatment is provided.

the collection and use of Henrietta L acks’ cells in research
E

was a legal practice in the 1950s, it would not happen

today. Today, she would be required to provide informed

consent to authorize their use for any purpose.

HeL a cells were the rst human cell line to be cultured

for research into c ancer. The source of the cells was a ◂ Figure 2 Tuskegee

c arcinoma biopsy from her cervix. At the time, scientists Syphilis Study participants

252
 Cells

End of chapter questions

1. The table shows the area of membranes in a rat liver cell. 3. A study was c arried out to determine the relationship

s
between the diameter of a molecule and its movement

2
through a membrane. The graph shows the results of
Membrane component Area/µm

s
the study.

plasma membrane 1,780

e
rough endoplasmic reticulum 30,400 High

evom ot ytiliba

r
enarbmem a hguorht
mitochondrial outer membrane 7,470

mitochondrial inner membrane 39,600

y
nucleus 280

l
lysosomes 100

y
evitaler

n
other components 18,500

t
a. C alculate the total area of membranes in the

O
i
liver cell. [2]

Low

s
b. C alculate the area of plasma membrane as a 0 0.4 0.8 1.2 1.6

molecular diameter / nm
percentage of the total area of membranes in the

y
cell. Show your working. [3]
a. From the information in the graph alone, describe
e
the relationship between the diameter of a
c. Explain the difference in area of the inner and outer

p
molecule and its movement through a
mitochondrial membranes. [3]
v

membrane. [2]

o
d. Using the data in the table, suggest two of the main
i

A second study was carried out to investigate the effect

activities of livercells. [2]
n

of passive protein channels on the movement of glucose

2. In human secretory cells, for example in the lung and

into cells. The graph shows the rate of uptake of glucose

the pancreas, positively charged ions are pumped out,

into erythrocytes by simple diffusion and facilitated

U

and chloride ions follow passively through chloride

diffusion.
n

channels. Water also moves from the cells into the liquid

that has been secreted. In the genetic disease cystic

500
/ e k a tp u

fibrosis, the chloride channels malfunction and too few 450

o

1–
d

facilitated diffusion
rh sllec

400
ions move out of the cells. The liquid secreted by the

350
cells becomes thick and viscous, with associated health
i
r

e s o c u lg

300

problems.
t

3–

250
o

mc

a. State the names of the processes that: 200

a

l omm

150
fo

i move positively charged ions out of the

f

100
etar
u

secretory cells [1]

50
simple diffusion
x

0
0

01

11

21

31

41

51

61

71

ii move chloride ions out of the secretory cells [1]

l
O

–3
iii move water out of the secretory cells. [1] external concentration of glucose / mmol dm
a

b. Explain why the fluid secreted by people with cystic

b. Identify the rate of glucose uptake at an external
v

fibrosis is thick and viscous. [4] –3

glucose concentration of 4 mmol dm

E

i simple diffusion. [1]

ii facilitated diffusion. [1]

253
 B Fo r m and function

s
s
3 Organisms

e
r
The form of an organism is its shape and underlying

P
s t r u c t u re. The o v e ra l l form of an organism is referre d to

y
as its morphology and the form of its individual organs

l
is its a n a t o my. The functioning of an organism is referre d

n
to as its p hys i o l o g y. Multicellular organisms h av e

t
specialized organs and organ s ys t e m s whose structure

O
i
is often well adapted to their functions. Ad a p t a t i o n s are

s
forms that correspond to functions. These adaptations

y
p e rs i s t f rom g e n e ra t i o n
e to g e n e ra t i o n bec ause they

inc re ase the chances of surviv al to reproductive a g e.

p
The blue whale is the largest animal to h av e ever lived,
v

including all the d i n o s a u rs . The blue whale he art be ats at

o
i

a s l ow ra t e ; at the surface the he art be ats about 30 times

n

per m i n u t e. When diving, it c an s l ow d ow n to about

6be ats per m i n u t e.

U

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v
E
B3.1 G as exchange

How are multicellular organisms adapted to c arry out gas exchange?

s
All organisms absorb the gasses they need from

s
their environment and release other gases into the

e
environment as waste products. What are the gases

that need to be exchanged? Which processes require

r
these gases and which processes generate them?

What is the importance of surface area-to-volume ratio

y
for cells? What challenges do multicellular organisms

have when it comes to gas exchange? How is it that the

l
sh in the water c an freely exchange gasses withthe

n
water but the snorkeler needs a connection to the

atmosphere?

O
i
▴ Figure 1 Snorkelers c an swim with sh but still exchange gases

s
with the air above

y
e
What are the similarities and dierences in gas exchange between a owering plant

p
and a mammal?
v

o
The glass beads in water are spheres. Spheres have
i

the smallest surface area-to-volume ratio of any shape.

n

Shapes approximating to spheres provide the gas-

exchange surface in both mammals and owering

plants. By making the spheres very small, a huge

U

surface area relative to volume c an be generated.

n

Although there is similarity in shape, the gas-exchange

surfaces of mammals and owering plants are markedly

o
d

dierent. In what ways do these structures dier?

i
r

t
o

▸ Figure 2 Glass beads in water

f

u
x

SL and HL AHL only

B3.1.1 G as exchange as a vital function in all organisms B3.1.11 Adaptations of foetal and adult haemoglobin for the
l
O

B3.1.2 Properties of gas-exchange surfaces transport of oxygen

a

B3.1.3 M aintenance of concentration gradients at exchange B3.1.12 Bohr shi

surfaces in animals B3.1.13 Oxygen dissociation curves as a means of

v

B3.1.4 Adaptations of mammalian lungs for gas exchange representing the anity of haemoglobin for oxygen at
E

B3.1.5 Ventilation of the lungs dierent oxygen concentrations

B3.1.6 Measurement of lung volumes

B3.1.7 Adaptations for gas exchange in leaves

B3.1.8 Distribution of tissues in a leaf

B3.1.9 Transpiration as a consequence of gas exchange in

a leaf

B3.1.10 Stomatal density

255
 Form and function

B3.1.1 Gas exchange as a vital function in all

organisms

All organisms absorb one gas from the environment and release another

one. This is gas exchange. Redwood trees absorb c arbon dioxide for use in

s
photosynthesis and release oxygen produced in the process. Humans absorb

s
oxygen for cell respiration and release the c arbon dioxide produced. Terrestrial

organisms exchange gases with the air. Aquatic animals such as sh exchange

e
gases with water.

r
Diusion is the basis of gas exchange. Bec ause the molecules move randomly,

P
diusion is a relatively slow process. G as exchange is only rapid enough if it

y
occurs over a large surface area and the distance across which the gases must

diuse is short. Unicellular and other small organisms have a large surface area-

l
to-volume ratio and the distance between the centre of the organism and the

n
exterior environment is small. They c an therefore use their outer surface for gas

t
exchange. In larger organisms, the surface area-to-volume ratio is smaller and

O
the distance between the centre of an organism and the exterior is greater. A

i
specialized gas-exchange surface is required that is much larger than the outer

s
surface, for example alveoli in lungs or the spongy mesophyll in a leaf.

y
e

p
B3.1.2 Properties of gas-exchange surfaces
v

Gas-exchange surfaces share four properties. They are:

o
i

• permeable — oxygen and c arbon dioxide c an diffuse across freely

▴ Figure 3 Axolotls develop lungs but

n

• large — the total surface area is large in relation to the volume of the organism
also retain their feathery external gills into

adulthood. The gill laments have a large

• moist — the surface is covered by a film of moisture in terrestrial organisms so

U

total surface area with a distance of 10 µm

gases c an dissolve

between blood in c apillaries and the water

n

• thin — the gases must diffuse only a short distance, in most c ases through a
outside. Axolotls are critic ally endangered

single layers of cells.

in their habitat in Mexico
o
d

i
r

ATL Thinking skills: The reasonableness ofknowledge claims: The surface area of
t
o

axolotl gills
a
f

The total surface area of alveoli in the lungs is oen said • C an you find evidence-based values for the number
u
x

to be the size of a tennis court, without any evidence for and mean surface area of human alveoli?

this. To estimate the surface area, we need to know how

• What numbers are needed to c alculate an estimate

l

many alveoli there are in the lungs and what their average
O

for the total surface area of an axolotl’s gills?

a

surface area is.

v

B3.1.3 M aintenance of concentration

E

gradients at exchange surfaces in animals

Diusion of gases only happens if there are concentration gradients. For

example, oxygen diuses from air in the alveoli to the adjacent c apillaries

bec ause the oxygen concentration of blood in the c apillaries is lower than

in air. C arbon dioxide diuses from the blood to air in the alveoli bec ause

256
 Organisms

there is a lower concentration of c arbon dioxide in the air. Diusion evens out

concentration gradients, which could slow and then stop gas exchange. For

gases to continueto diuse across exchange surfaces, concentration gradients

must be maintained.

s
In small, aerobic ally respiring organisms that use their outer surface for gas

exchange, it is cell respiration that maintains concentration gradients. This

s
process continuously uses oxygen and produces c arbon dioxide, so the

e
oxygen concentration within the organism remains lower than outside and the

c arbon dioxide concentration remains higher. In larger organisms such as sh

r
or mammals, blood ows continuously through dense c apillary networks in the

organs specialized for gas exchange. Due to aerobic respiration, this blood has a

y
low concentration of oxygen and a high concentration of c arbon dioxide.

l
Ventilation also helps to maintain concentration gradients. This term was

y
originally used for the movement of air in and out of the lungs, but it is now also

n
used to refer to movement of water across gills.

O
• M ammals periodic ally expel air from the alveoli by exhaling and then replace

i
it by inhaling fresh air. This prevents the oxygen concentration from dropping

s
too low for diffusion from the air to the blood and also prevents the c arbon

dioxide concentration from rising too high. The rate of ventilation is adjusted

y
according to the c arbon dioxide concentration of the blood. e
• Fish take in fresh water through their mouth and pump it over their gills and

p
then out through the gill slits. This one-way flow of water, combined with
v

blood flow in the opposite direction, ensures that the oxygen concentration

in the water adjacent to the gills remains high and the c arbon dioxide

o
i

concentration remains low.

n

Data-based questions: Concentration gradients

U

Figure 4 shows the typic al composition of atmospheric 1. Explain why the oxygen concentration in the alveoli is

air, air in the alveoli and gases dissolved in air returning to not as high asinfresh air that is inhaled. [2]

the lungs in the pulmonary arteries.

o
d

2. a. C alculate the difference in oxygen

concentration between air in the alveolus

e
i
r

oxgen and blood arriving at the alveolus. [1]

c arbon dioxide
t

b. Deduce the process c aused by this

o

nitrogen

concentration dierence. [1]

a

700

c. i. C alculate the dierence in c arbon

f

59
gH mm / erusserp

600
u

570 570 565

dioxide concentration between air
x

500 inhaled and air exhaled. [1]

l

ii. Explain this dierence. [2]

O

400
a

d. Despite the high concentration of nitrogen

300
in air in alveoli, little or none diuses from
v

the air to the blood. Suggest reasons forthis. [2]

l a i t r ap

200

159

120
105
E

100

45
40 40
27

atmospheric air in blood air exhaled

air that is alveoli travelling

inhaled to alveoli

▴ Figure 4

257
 Form and function

trachea
B3.1.4 Adaptations

of mammalian lungs

for gas exchange

s
All mammals use lungs for gas

right bronchus
exchange, even marine species such

s
as whales and dolphins. Air is drawn
intercostal muscle

e
into the lungs through the trachea

(windpipe) and then the le and

r
right bronchi (singular, bronchus). In

each lung, the bronchus branches

y
repeatedly to form bronchioles.
ribs

Alveolar ducts branch o from the

l
bronchioles, each leading to a

n
group of ve or six alveoli (air-sacs).

right lung bronchioles

t
A pulmonary alveolus has a diameter

O
diaphragm

i
of 0.2 mm to 0.5 mm, but its wall

s
is a single layer of cells, much of

which is only about 0.2 µm thick.

▴ Figure 5 Airways, lungs and associated muscles in the human thorax

y
e Alveoli are surrounded by a dense

c apillary network. The c apillary wall

p
is also extremely thin and consists
thin AT1 cell which
v

of a single layer of cells. Air and

allows rapid gas

o
blood are therefore a very short
exchange
i

distance apart. The c apillaries cover

n

much of the surface of the alveoli

but there are also some other cells.

alveolar duct

Some of these have collagen bres

U

to strengthen the lung tissue and

n

elastic bres to help limit inhalation

and c ause passiveexhalation.

o
d

i
r

phagocyte m
t

0
o

0
5
–
0
a

0
2
f

u
x

l
O

a
v
E

network of blood AT2 cell which

capillaries secretes surfactant

▴ Figure 6 Structure of an alveolus

258
 Organisms

An individual alveolus provides a small surface area for gas exchange, but

bec ause there are so many of them — about 300 million in a pair of adult

lungs — the total area is very large: about 40 times greater than the outer surface

of the body. The surface area of the basket-like networks of blood c apillaries

around the alveoli is almost as large as that of the alveoli.

s
Cells in the wall secrete a pulmonary surfactant. Its molecules have a structure

s
similar to that of phospholipids in cell membranes. They form a monolayer on the

e
surface of the moisture lining the alveoli, with the hydrophilic heads facing the

water and the hydrophobic tails facing the air. This reduces the surface tension

r
and prevents the water from c ausing the sides of the alveoli to adhere when air is

exhaled from the lungs. This helps to prevent collapse of the lung.

y
air in alveolus

l
water

monolayer of

y
surface

n
surfactant

O
i
s
▴ Figure 7 Pulmonary surfactant molecules on the surface of the lm of

moisture lining the alveoli

y
e

p
Data-based questions: COPD and gas exchange
v

In healthy lung tissue, there are open airways and

groups of small thin-walled alveoli. Chronic obstructive

o
i

pulmonary disease (COPD) is a group of irreversible

n

lung conditions that are associated with smoking and

air pollution. Patients with COPD have airways that have

U

become narrow and a smaller number of larger air sacs.

n

1. a. Place a ruler across each micrograph and count

how many times the edge of the ruler crosses a

o
d

gas-exchange surface. Repeat this several times

for each micrograph, in such a way that the

i
r

results are comparable. Tabulate your results

t

andc alculate means. [3]

o

b. Explain the conclusions that you draw from

a

theresults. [3]
f

2. People who have COPD feel tired all the time.

x

Explainthe reasons for this. [3]

l
O

3. People with COPD often have an enlarged and

a

strained right side of the heart. Suggest areason

forthis. [1]
v
E

▸ Figure 8 Healthy lung tissue (top) and lung

tissue from a person with COPD (bottom)

259
 Form and function

B3.1.5 Ventilation of the lungs

The airways that connect the lungs to the air outside the body consist of the nose,

mouth, trachea, bronchi and bronchioles. The trachea and bronchi have c artilage

in their walls to ensure they remain open. The bronchioles have smooth muscle

s
bres in their walls, allowing the width of these airways to vary.

s
Ventilation of the lungs involves some basic physics. If particles of gas spread out

to occupy a larger volume, the pressure of the gas becomes lower. Conversely,

e
if a gas is compressed to occupy a smaller volume, the pressure rises. If gas is

r
free to move, it will always ow from regions of higher pressure to regions of

lowerpressure.

y
During ventilation, muscle contractions c ause the pressure inside the thorax to

drop below atmospheric pressure. As a consequence, air is drawn into the lungs

l
y
from the atmosphere (inspiration) until the lung pressure has risen to atmospheric

n
pressure. Other muscle contractions then c ause pressure inside the thorax to

t
rise above atmospheric, so air is forced out from the lungs to the atmosphere

O
(expiration), helped by the recoil of elastic bres in lung tissue that become

i
stretched during inspiration.

s
r

y
Inspiration Expiration
tnemevom mgarhpaid

p
tnemevom

v
tnemevom

o
i
egacbir

C
ria

n
o
d

Diaphragm The diaphragm contracts and so it moves The diaphragm relaxes so it c an be pushed upwards

downwards and pushes the abdomen wall out into a more domed shape
i
r

Abdomen Muscles in the abdomen wall relax allowing Muscles in the abdomen wall contract pushing the
t

wall pressure from the diaphragm to push it outwards abdominal organs and diaphragm upwards (but
o

muscles only during forced expiration)

f

External The external intercostal muscles contract, pulling The external intercostal muscles relax and are pulled
u
x

intercostal the ribc age upwards and outwards into their elongated state

muscles
l
O

Internal The internal intercostal muscles relax and are pulled The internal intercostal muscles contract, pulling the
a

intercostal into their elongated state ribc age inward and downwards (but only during

muscles forced expiration)

v

Volume or The volume inside the thorax increases and The volume inside the thorax decreases and
E

pressures consequently the pressure decreases, sucking air in consequently the pressure increases, forcing air out

▴ Figure 9 Muscle actions that c ause inspiration and expiration

260
 Organisms

B3.1.6 Measurement of lung volumes

• Tidal volume is the volume of fresh air that is inhaled and also the amount of

stale air that is exhaled with each ventilation. Ventilation rate is the number of

times that air is drawn in or expelled per minute.

s
• Vital c apacity (or forced vital c apacity) is the total volume of air that c an be

s
exhaled after a maximum inhalation or the total volume of air that c an be

inhaled after a maximum exhalation.

e
• Inspiratory reserve volume is the amount of air a person c an inhale forcefully

after normal tidal volume inspiration.

r
• Expiratory reserve volume is the amount of air a person c an exhale forcefully

y
after a normal exhalation.

l
These lung volumes c an be measured using either simple apparatus or

y
specialized meters. Simple apparatus is shown in Figure 10. One normal breath

n
is exhaled through the delivery tube into a vessel and the volume is measured.

t
It is not safe to use this apparatus for repeatedly inhaling and exhaling air as the

O
c arbon dioxide concentration will rise too high.

i
s
r

y
e

p
bell jar with
v

graduations

o
i

delivery tube
n

pneumatic trough
U

▴ Figure 11 A oat spirometer has an air reservoir oating on

▴ Figure 10 Simple apparatus for measuring the volume of air

o

water. Air in the reservoir c an be breathed in and out through

d

exhaled. How could it be modied to measure volumes inhaled?

a tube with a mouthpiece on the end. Exhaled air passes back

into the reservoir via alkali that absorbs c arbon dioxide. This
i
r

prevents the concentration of c arbon dioxide from rising with

t

repeated breaths
o

Specially designed spirometers measure ow rate into and out of the lungs
f

and from these measurements lung volumes c an be deduced. There are many
x

dierent designs, some of which c an be used with data logging soware.

l
O

ATL Communic ation skills: Deciphering meanings by knowing etymology

v

Etymology is the study of the origin of words. What • fundere means “to pour ”
E

biologic al terms are derived from these L atin words?

• diffundere means “to pourapart”

• pulmonarius means “lung”

Why do so many terms in biology and medicine have

• alveus means “hollow vessel” L atin origins?

• ventus means “wind”

261
 Form and function

B3.1.7 Adaptations for gas exchange inleaves

Chloroplasts need a supply of c arbon dioxide for photosynthesis. The oxygen

produced during the process of photosynthesis must be removed. A large area

of moist surface is required over which c arbon dioxide c an be absorbed and

s
oxygen excreted — this is provided by the leaves. A challenge for plants is to

avoid excessive loss of water from the surface, so leaves are adapted for both gas

s
exchange and water conservation.

e
The outer surface of the leaf is covered in a layer of wax, secreted by the

r
epidermis cells. This waterproof layer is c alled the waxy cuticle. It varies in

thickness between plants and is particularly thick on the upper surface of leaves

y
and in plants adapted to dry habitats.

The waxy cuticle has low permeability to gases, but within the epidermis there

l
y
are pairs of guard cells, which c an change their shape either to open up a pore

n
or to close it. The pore is c alled a stoma (plural, stomata) and it allows c arbon

t
dioxide and oxygen to pass through. The guard cells usually close the stomata

O
at night when photosynthesis is not occurring and gas exchange is not required.

i
▴ Figure 12 One of the two stomata is

They also close the stomata if a plant is suering water stress and is in danger of
open and the other is closed in this sc anning

s
dying from dehydration.
electron micrograph of the outer surface of

r
a lavender plant leaf. The epidermis cells

y
have sinuous edges, with ridges of thick
e
wax visible on their surfaces

p
upper epidermis
v

palisade mesophyll

o
i

with tightly packed

n

cylindric al cells

leaf vein
U

spongy mesophyll

with rounded cells and guard cell

o

extensive air space

d

lower epidermis
r

▴ Figure 13 Sc anning electron micrograph of a leaf of Prunus. The leaf was frozen and then
o

fractured so the interior structure is visible

f

u
x

The stomata connect the air outside to a network of air spaces in the spongy

mesophyll of the leaf. C arbon dioxide and oxygen c an diuse through these air
l
O

spaces. The walls of the spongy mesophyll cells provide a very large total surface
a

area for gas exchange. Bec ause these walls are permanently moist, c arbon

dioxide in the air spaces c an dissolve and then diuse through the mesophyll
v

cells. Photosynthesis uses c arbon dioxide, generating a concentration gradient

from the air outside the leaf to the chloroplasts in mesophyll cells. Photosynthesis
E

raises the concentration of oxygen in chloroplasts, so it diuses to the surfaces of

spongy mesophyll cells and then into the air spaces and out of the leaf.

Inevitably, there is some loss of water by evaporation from the moist spongy

mesophyll cell walls and diusion out through the stomata. There is also some
▴ Figure 14 Veins in a leaf of Gunnera

use of water in photosynthesis. Water is supplied to the leaf in xylem vessels,

manicata

loc ated in the leaf veins (Figure 14).

262
 Organisms

B3.1.8 Distribution of tissues in a leaf

Plan diagrams show the areas of tissues, but not individual cells. The lines indic ate

the junctions between tissues.

upper

s
epidermis

s
palisade
xylem

e
mesophyll

r
spongy

mesophyll

P
phloem

y
◂ Figure 15 An example of a tissue plan of

lower

l
a typic al dicotyledonous leaf, with the leaf in

epidermis

y
transverse section

n
t
Data-based questions: Sun and shade leaves

O
i
On many trees there are dierences in structure between

s
leaves on upper branches that are in full sunlight and

y
leaves on the same tree that are lower down and shaded.
e
1. Draw plan diagrams of the tissues in a representative

p
part of each of the Prunus leaves. [7]
v

2. Compare and contrast the structure of the two

leaves,including overall thickness, thickness of

o
i

waxycuticle and the structure of the palisade

n

mesophyll and spongy mesophyll. [4]

3. a. Deduce which leaf grew in the sun and

U

whichinthe shade. [1]

n

b. Discuss reasons for the dierences between

sunand shade leaves. [3]

o
d

▸ Figure 16 Micrographs of two leaves of Prunus caroliniana,

i

one that grew in the sun and one that grew in the shade. The
r

micrographs have the same magnic ation

t
o

B3.1.9 Transpiration as a consequence of

f

gas exchange in a leaf

x

Exchange of oxygen and c arbon dioxide only works eectively if the gas-
l
O

exchange surface is moist. Water evaporates from a moist surface unless

a

the air is already saturated. Evaporation is the separation of individual water

molecules from liquid water, so the molecules become part of a gas. Molecules
v

in this separated state are c alled water vapour. The opposite process is

condensation — water vapour molecules join others to become liquid.

E

If the air is very humid and the number of water molecules evaporating is equalto

the number condensing, we say the air is saturated with water vapour. There will

be no net loss from a gas-exchange surface. The amount of water vapour that

air c an hold when it is saturated varies with temperature. This is bec ause there

is more energy available to break hydrogen bonds between water molecules at

higher temperatures.

263
 Form and function

4.0%

retaw fo ssam yb

tniop
3.0%

noitarutas ta

s
2.0%

s
egatnecrep
▸ Figure 17 Graph showing

e
the maximum percentage,

ria
by mass, of water vapour
1.0%

ni

r
that air c an hold at sea-level

pressure between −60°C and

y
+40°C. At lower air pressures, 0.0%

–60 –40 –20 0 20 40

the percentages at each

l
temperature / °C
temperature would be higher

n
t
The walls of the spongy mesophyll inside a leaf are kept moist for gas exchange.

O
Some of this water will evaporate unless the air spaces are already saturated with

i
water vapour. Unless the concentration of water vapour in the air outside the

s
leaf is as high as the concentration in the air spaces, water vapour will diuse out

r
through the stomata. This c auses the humidity of the air spaces to drop below the

y
saturation point, so more water evaporates from spongy mesophyll cell walls. The
e
loss of water vapour from the leaves and stems of plants is c alled transpiration.

p
v

Transpiration rates are aected by environmental factors.

• Temperature (positive correlation): at

o
higher temperatures there is more
i

energy available for evaporation. Also warmer air c an hold more water
n

vapour before becoming saturated.

• Humidity (negative correlation): the higher the relative humidity of the air, the
U

smaller the concentration gradient of water vapour between the air spaces
n

inside the leaf and the air outside, so the lower the rate of diffusion. There is

no transpiration if the air outside the leaf is saturated with water vapour.
o
d

Plants minimize water losses using guard cells. These cells are found in pairs, one

on either side of a stoma. Guard cells control the aperture of the stoma and c an
i
r

adjust from wide open to fully closed. Plants c an prevent nearly all transpiration
t

by closing their stomata. Most plants do this routinely at night when there is no
o

photosynthesis. The disadvantage of closing the stomata in daylight is that little

or no c arbon dioxide c an be absorbed, so the rate of photosynthesis is limited.

f

Control mechanisms in the guard cells allow the aperture of the stomata to be
x

varied according to the c arbon dioxide concentration inside the leaf. Rising

atmospheric c arbon dioxide concentrations due to human activity are allowing

l
O

plants to open stomata less widely, easing the problem of water loss a little.
▴ Figure 18 Open and closed stomata
a
v

B3.1.10 Stomatal density

E

Stomatal density is the number of stomata per unit area of leaf surface. To nd the

density, the number of stomata in a known area must be counted. Guard cells

and stomata are too small to be seen with the naked eye but are easily visible with

a microscope.

264
 Organisms

Two techniques c an be used.

1. A sample of epidermis is peeled off the leaf. This is easy with Commelina and

Tradescantia. Other species are worth trying. The leaf c an be folded across

to break all the tissues apart from the lower epidermis and then the epidermis

c an be peeled off or the leaf c an be torn in half obliquely which often

s
separates areas of epidermis. Small areas of epidermis are then mounted in

s
water on a microscope slide and are examined.

e
2. Another technique c an be used if the leaf is non-hairy and smooth.

Colourless nail varnish is painted on to a small area of upper epidermis and

r
lower epidermis. When it is dry, the nail varnish is peeled off, mounted on

a microscope slide and examined. The nail varnish forms a c ast of the leaf

y
surface, with the margins of the cells and the stomata clearly visible.

l
The microscope slide should be moved until the eld of view is lled by the

n
peeled epidermis or leaf c ast. The number of stomata c an then be counted.

Repeat counts should be c arried out and a mean number of stomata c alculated. If

t
the area of the eld of view is determined, the stomatal density c an be c alculated.

O
i
▴ Figure 19 The lower epidermis c an

meannumberofstomata
2
usually be peeled more easily than the

s
stomatal density (mm ) =
2

areaofeldofview(mm )
upper epidermis

y
e
Applying techniques: Using a potometer to measure rates of transpiration

p
v

Mechanisms involved in water transport in the xylem c an

be investigated using apparatus and materials that show

o
i

similarities in structure to plant tissues. Figure 20 shows

n

a potometer. This is a device used to measure water

uptake in plants. The apparatus consists of a leafy shoot in

U

a tube (right), a reservoir (le of shoot), and a graduated

n

c apillary tube (horizontal). A bubble in the c apillary tube

marks the zero point. As the plant takes up water through

its roots, the bubble will move along the c apillary tube.
o
d

The distance the bubble travels and the time taken are

measured. The tap below the reservoir allows the bubble

i
r

to be reset to c arry out new measurements.

t
o

▴ Figure 20 A potometer
f

u
x

l
O

Measurement: Repeat measurements to improve reliability

a

It is standard practice in scientic research to repeat Repeating the counts has several advantages. It helps
v

measurements and replic ate trials. In this c ase, samples avoid the danger of an outlier having a disproportionate

should be taken from as many leaves on the plant and as eect on the conclusions. It increases reliability bec ause
E

many plants of the species as possible. For each leaf, as it allows a mean to be c alculated which will be closer to

many areas as possible should be examined and a count the true stomatal density than a single count is likely to

of the number of stomata taken in each area. The counts be. It also allows the reliability of the mean to be assessed

will not be the same, but if done c arefully, each count will statistic ally. The less variation between the repeats, the

be correct. The variability is natural in biologic al material. more reliable the mean.

265
 Form and function
LHA

B3.1.11 Adaptations of foetal and adult

haemoglobin for the transport of oxygen

Haemoglobin is the oxygen transport protein c arried by red blood cells. Oxygen

binds reversibly to haemoglobin. E ach of the four subunits in a haemoglobin

s
molecule has a haem group which acts as a binding site, so up to four molecules

s
of oxygen c an be transported per haemoglobin molecule.

e
Binding is cooperative in a haemoglobin molecule, bec ause when oxygen binds

to one haem group, conformational changes are c aused that increase the oxygen

r
anity of the other haem groups. Conversely, when an oxygen dissociates,

P
it c auses conformational changes that reduce anity in other haem groups.

y
The two most probable states for a haemoglobin molecule are therefore fully

saturated with four oxygens bound (the R state), or unsaturated with no oxygen

l
bound (theT state).

n
The oxygen saturation level of haemoglobin is positively correlated with oxygen

O
concentration. The oxygen concentrations are given as partial pressures,

i
with kilopasc als as the pressure units. As partial pressure of oxygen rises,

s
percentage saturation rises until the partial pressure reaches 10 kPa, above which

haemoglobin becomes 100% saturated. This happens as blood ows through

y
the c apillaries surrounding e the alveoli, which have an oxygen concentration of

between 10 kPa and 13 kPa (in normal healthy lungs). Fully oxygenated blood

p
leaving the lungs is c arried to all other organs of the body, where the partial
v

pressure is usually below 10 kPa. At least some of the oxygen c arried by the

o
haemoglobin therefore dissociates (separates) and diuses into the tissues of
i

theorgan.
n

Bec ause of cooperative binding, oxygen saturation of haemoglobin is not

directly proportional to oxygen concentration. Instead, it changes from fully

U

saturated to unsaturated over a relatively narrow range of oxygen concentrations.

n

This ensures that haemoglobin unloads oxygen very readily in a tissue where

aerobic respiration has reduced the oxygen concentration. Without this

o
d

3 adaptation, concentrations of oxygen could not be kept as high as they are in

▴ Figure 21 Less than 50 cm of oxygen

3
respiring tissues, potentially reducing the activity of muscle and other tissues.
c an dissolve in 1 dm of water at 37°C, but
i

blood c an hold over 200 cm bec ause of the Haemoglobin is also adapted for oxygen transport by interacting with c arbon
r

oxygen binding c apacity of haemoglobin dioxide. The mechanisms for this are described in Section B3.1.12
t
o

a
nibolgomeah fo
f

u
x

this would be
O

negyxo htiw

the relationship
a

noitarutas

if oxygen

the actual relationship

saturation was
v

between saturation and

directly

oxygen concentration is not

proportional to

directly proportional with

E

concentration
egatnecrep

most of the increase over a

narrow range of oxygen

concentrations. This is a

sigmoid curve

oxygen concentration (usually shown as partial

pressures in kilopascals)

▴ Figure 22 Oxygen dissociation curve

266
 Organisms

LHA
Humans produce dierent types of haemoglobin before and aer birth. At

birth, a baby still has red blood cells with foetal haemoglobin. It takes several

months for all the red blood cells c arrying foetal haemoglobin to be replaced

with cells c arrying adult haemoglobin. Foetal haemoglobin has a stronger anity

for oxygen than adult haemoglobin. At any partial pressure of oxygen, foetal

s
haemoglobin is therefore more saturated with oxygen than adult haemoglobin.

During pregnancy a foetus obtains oxygen via the placenta. Oxygen dissociates

s
from haemoglobin in maternal blood in the placenta and binds to haemoglobin

e
in foetal blood. This c an only happen bec ause foetal haemoglobin has a stronger

anity for oxygen than adult haemoglobin.

r
P

y
B3.1.12 Bohr shi

l
Increased aerobic respiration in active tissues results in greater release of c arbon

n
dioxide into the blood. Increases in c arbon dioxide concentration decrease the

t
anity of haemoglobin for oxygen and therefore increase dissociation of oxygen

O
from haemoglobin. Two mechanisms c ause the decrease in anity.

i
1. C arbon dioxide and water are converted in red blood cells into hydrogen

s
ions and hydrogen c arbonate ions.

y
+

CO + H O → H + HCO
e
2 2 3

p
This reduces the pH of the blood, which reduces the affinity of haemoglobin
v

for oxygen. In the lungs where the concentration of c arbon dioxide is low,

the pH is 7.4. In active muscle, there is a higher c arbon dioxide concentration

o
i

and the pH typic ally is about 7.2. This small pH difference is enough to
n

promote oxygen binding to haemoglobin in the lungs and dissociation in

active respiring tissues.

U

2. E ach of the four subunits of haemoglobin c an react reversibly with

n

c arbon dioxide at the amino terminal of the polypeptide. The amine

group is converted to c arbamate and the haemoglobin becomes

o
d

c arbaminohaemoglobin.

haemoglobin + 4CO c arbaminohaemoglobin

i
r

2
t

This reaction reduces the affinity of haemoglobin for oxygen. Due to the
o

high c arbon dioxide concentration of actively respiring tissues, haemoglobin

is converted to c arbaminohaemoglobin, promoting release of oxygen.

f

C arbaminohaemoglobin changes back to haemoglobin in the lungs, due

x

to the low c arbon dioxide concentration. The haemoglobin then becomes

l

100% saturated as it is c arried in red blood cells through the alveolar

O

c apillaries. Another consequence of this mechanism is that haemoglobin

a

molecules c an each remove four c arbon dioxide molecules from respiring

v

tissues and transport them to the lungs.

The reduction in the affinity of haemoglobin for oxygen in high c arbon

E

dioxide concentrations is known as the Bohr shift or Bohr effect. It helps

to ensure that respiring tissues have enough oxygen when their need for

oxygen is greatest.

267
 Form and function
LHA

B3.1.13 Oxygen dissociation curves as

a means of representing the anity of

haemoglobin for oxygen at dierent

s
oxygen concentrations

s
Oxygen dissociation curves show the percentage oxygen saturation of

haemoglobin at dierent oxygen concentrations. Normal atmospheric pressure

e
is 101.3 kPa and as 21% of air is oxygen, the partial pressure of oxygen is 21.2 kPa.

r
The oxygen concentration inside the alveoli is lower, so oxygen dissociation

curves usually only cover a range from 0 kPa to 15 kPa. Figure 23 shows the

y
oxygen dissociation curve for adult haemoglobin. The sigmoid form of the curve

is due to cooperative binding.

l
y

n
t

O
i
s
r

y
e

p
v

o
i
n

C
U

▸ Figure 23 The oxygen dissociation curve

for adult haemoglobin is sigmoid bec ause of

o
d

the eects of cooperative binding

i
r

Figure 24 shows that the dissociation curve for foetal haemoglobin is sigmoid,
t
o

like adult haemoglobin, but the curve is further to the le. An oxygen saturation
a

curve that is displaced to the le indic ates increased anity for oxygen. Foetal

haemoglobin has a stronger anity than adult haemoglobin, so percentage

f

saturation is higher at every partial pressure of oxygen.

x

negyxo htiw
l
O

100

HbF
v

noitarutas
E

HbA
50
egatnecrep

▸ Figure 24 A comparison of the oxygen

0

dissociation curves of foetal (HbF) and 0 2 4 6 8 10

adult haemoglobin (HbA) partial pressure of oxygen / kPa

268
 Organisms

LHA
Figure 25 shows the oxygen dissociation curve for adult haemoglobin at two

dierent concentrations of c arbon dioxide. The curve for the higher c arbon

dioxide concentration is displaced to the right, showing a decreased anity

of haemoglobin for oxygen. This is c alled the Bohr shi (see Section B3.1.12)

and results in a greater release of oxygen from haemoglobin at the same partial

s
pressure ofoxygen.

s
negyxo htiw

100

e
3 kPa (Pco )
2

r
75

y
noitarutas

6 kPa (Pco )
2
50

l
y

n
egatnecrep

25

O
i
0

s
5 10 15

r
partial pressure of oxygen / kPa

y
e
▴ Figure 25 The Bohr shi

p
v

o
i

Linking questions
n

1. How do multicellular organisms solve the problem of access to materials

for all their cells?

U

a. Outline the relationship between surface area and volume and the
n

exchange of materials between cells and their environment. (B2.3.6)

o

b. O utline the role of the circulatory system in the distribution of

d

materials in the body. (B3.2.1)

i
r

c. Describe the role of diusion in gas exchange. (B2.1.3)

t
o

2. What is the relationship between gas exchange and metabolic processes

a

in cells?
f

a. Outline the movement of gases between c apillaries and alveoli.

x

(B3.1.1)
l
O

b. List metabolic processes that produce c arbon dioxide in the human

a

body. (C1.2.11)

c. Explain the role of oxygen in the mitochondrial electron transport

v

chain. (C1.2.16)
E

269
 B3.2 Transport

s
What are the dierences and similarities between transport in animals and plants?

s
Figure 1 shows a “nodding donkey”—a tool for drawing

underground oil to the surface. Initially oil ows up a well bec ause

e
of pressure in the oil-bearing rock, but eventually a pump is

needed at the bottom of the well to pull the oil out of the well.

r
Are uids only pushed in mammalian circulatory systems or are

y
they sometimes drawn? Why is uid, like blood or sap, necessary

for transport materials? To what extent is the movement of uid

l
in xylem and phloem like the closed circulatory system found in

y
organisms like mammals? C an phloem and xylem be thought

n
of as one circulatory system or two? What is the role of pressure

▴ Figure 1 A “nodding donkey”

t
dierences in plant and animal circulatory systems?

O
for bringing oil to the surface

i
s
What adaptations facilitate transport of uids in animals and plants?

y
Figure 2 is a satellite image showing the delta of
e
the Lena River in Siberia. The reticulate pattern of

p
channels in the Lena delta is reminiscent of blood
v

c apillaries or venation in a leaf. What role do pressure

o
gradients play in the movement of uids in living
i

things and in rivers? What is the reason that vessel

n

walls are typic ally structurally strengthened? Are there

common features that plant and animal vessels have

U

to reduce resistance to ow? What mechanisms exist

◂ Figure 2 The delta

n

to ensure that all parts of a plant or animal receive

for the Lena River

sucient quantities of the materials that they require?

in Siberia
o
d

SL and HL AHL only

i
r

B3.2.1 Adaptations of c apillaries for exchange of materials B3.2.11 Release and reuptake of tissue uid in c apillaries
t

between blood and the internal or external environment B3.2.12 Exchange of substances between tissue uid and
o

B3.2.2 Structure of arteries and veins cells in tissues

B3.2.3 Adaptations of arteries for the transport of blood B3.2.13 Drainage of excess tissue uid into lymph ducts
f

away from the heart B3.2.14 Dierences between the single circulation of bony
x

B3.2.4 Measurement of pulse rates sh and the double circulation of mammals

B3.2.5 Adaptations of veins for the return of blood to B3.2.15 Adaptations of the mammalian heart for delivering
l
O

the heart pressurized blood to the arteries

a

B3.2.6 C auses and consequences of occlusion of the B3.2.16 Stages in the c ardiac cycle

coronary arteries B3.2.17 Generation of root pressure in xylem vessels by

v

B3.2.7 Transport of water from roots to leaves during active transport of mineral ions
E

transpiration B3.2.18 Adaptations of phloem sieve tubes and companion

B3.2.8 Adaptations of xylem vessels for transport of water cells for transloc ation of sap

B3.2.9 Distribution of tissues in a transverse section of the

stem of a dicotyledonous plant

B3.2.10 Distribution of tissues in a transverse section of the

root of a dicotyledonous plant

270
 Organisms

B 3 . 2 .1 Ad a p t a t i o n s of c apillaries for

exc h a n g e of materials between

blood and the internal or ex t e r n a l

s
e nv i r o n m e n t

s
C apillaries are the narrowest blood vessels with a diameter of about 10 μm. They

branch and rejoin repeatedly to form a c apillary network with a huge total length.

e
C apillaries transport blood through almost all tissues in the body. Two exceptions

are the lens and the cornea of the eye — these tissues must be transparent so there

r
are no blood vessels.

y
M any narrow c apillaries have a total surface area that is greater than fewer wider

blood vessels. This means that the c apillary network in any tissue increases

l
y
the scope for diusion between the blood and the tissue cells. The density of

n
c apillary networks in dierent tissues depends on the needs of the cells, but all

t
active cells in the body are close to a c apillary.

O
i
The c apillary wall consists of one layer of endothelium cells (see Figure 3 on the

s
next page). This layer of cells has a coating of extracellular brous proteins which

are crosslinked to form a gel. The gel is c alled the basement membrane and it

y
acts as a lter that allows small or medium-sized particles to pass through, but not
e
macromolecules. There are pores between the epithelium cells, so the c apillary

p
wall is very permeable. The pores allow part of the blood plasma, but not the red
v

blood cells, to leak out through the basement membrane.

o
i

The uid that leaks out is very similar but not identic al in composition to blood

plasma. It is c alled tissue uid. Tissue uid contains oxygen, glucose and all other
n

substances in blood plasma except large protein molecules, which are too large

to pass through the basement membrane. The uid ows between the cells in a
U

tissue, allowing them to absorb useful substances and excrete waste products.
n

The tissue uid then re-enters the c apillary network.

In some tissues, there are greater numbers of very large pores in the c apillary
o
d

walls. These are c alled fenestrated c apillaries. Fenestrated c apillaries allow larger

volumes of tissue uid to be produced, which speeds up exchange between

i
r

the tissue cells and the blood. The glomerulus (lter unit) of the kidney has
t
o

fenestrated c apillaries so it c an produce large volumes of ltrate in the rst stage

a

of urine production.
f

u
x

l
O

a
v
E

271
 Form and function

red blood
blood

cell
plasma

basement membrane –

a mesh of fibrous

proteins forming a gel

s
that acts as a filter

s
epithelium cells

e
forming the wall of

the capillary—very

r
thin except where the

pore between nucleus of a cell is

y
epithelium cells located

allowing fluid to

nucleus of

l
leak out through

y
epithelium

n
the basement

cell

membrane

O
10 µm
▸ Figure 3 Structure of a c apillary

i
s
r
B3.2.2 Structure of arteries and veins

y
e
Arteries c arry pulses of high-pressure blood away from the heart to the organs

p
of the body. Veins c arry a stream of low-pressure blood from the organs to the
v

heart. Bec ause of the dierence in function, these two types of blood vessel have

o
a dierent structure to their walls (Figure 4).
i
n

C
U

n
o
d

▾ Table 1 Dierences in structure of the

i
r

walls of arteries and veins

t
o

Arteries Veins
a

Thicker wall Thinner wall

f

Narrower lumen Wider lumen

x

Circular in Circular or
l

section attened in
O

section

Inner surface No inner surface ▴ Figure 4 An artery (upper le) and a vein (lower right) are
v

surrounded by adipose (fat storage) tissue. The tissue below is muscle

corrugated corrugation
E

Fibres visible in Few or no bres

Table 1 lists the distinguishing features of arteries and veins that are easily
the wall visible in the wall

distinguishable in micrographs.

272
 Organisms

B3.2.3 Adaptations of arteries for the

transport of blood away from the heart

The wall of the artery is composed of several layers:

s
• tunic a externa — a tough outer layer of connective tissue with collagen fibres

s
• tunic a media — a thick layer containing smooth muscle and elastic fibres

made of the protein elastin

e
• tunic a intima — a smooth endothelium forming the lining of the artery;

r
insome arteries the tunic a intima also includes a layer of elastic fibres.

E ach time the ventricles of the heart pump, a burst of blood under high pressure

y
enters the arteries and ows along them. The pressure then declines until the next

heartbeat. Arteries have relatively narrow lumens, which helps them to maintain

l
high blood pressures and high velocities of blood ow.

n
Artery walls are relatively thick and contain elastic bres and tough collagen

t
bres. The elastic bres are proteins that c an stretch and then recoil. Collagen

O
i
bres are tough rope-like proteins with high tensile strength. These features make

s
arteries strong enough to withstand high and variable blood pressures without

bulging outwards (known as an aneurysm) or bursting.

y
Elastic bres make up as much as 50% of the dry mass of artery walls. Peak
e
pressure in an artery (systolic pressure) c auses the wall of an artery to be pushed

p
outwards, widening the lumen and stretching the wall. When stretched, elastic
v

bres store potential energy. At the end of each heartbeat the pressure in arteries

falls and the stretched elastic bres return the energy by recoiling and squeezing
o
i

the blood in the lumen. In this way, the elastic bres help to reduce the amount of
n

energy expended in transporting blood to the organs of the body.

U

tunica externa tunica media

n

outer thick layer of

coat of tough smooth muscle tunica

tunica media
o
d

collagen fibres cells, elastic externa—

—thin layer of

and elastic tissue and relatively thick

elastic tissue and
i

tissue collagen fibres

r

tough outer
collagen fibres
t

coat
o

a
f

u
x

thicker wall in

arteries than
l
O

veins
a
v

lumen

tunica intima
E

the space inside

an endothelium made of a

the artery

single layer of cells with

tunica
through which lumen—

extra elastic tissue near

intima
blood flows— relatively

the heart

relatively narrow wide

▴ Figure 5 Tissue plan diagrams of artery and vein in transverse section

273
 Form and function

When the elastic bres are recoiling and pushing on blood in an artery, the

semilunar valves at the exit of the ventricles are closed. This means that blood

c annot ow back towards the heart, it is forced onwards towards the organs.

Elastic bres therefore help to pump blood along the arteries and prevent the

minimum pressure inside the artery (diastolic pressure) from becoming too low.

s
They help to even out blood ow in the arteries.

s
Artery walls also contain smooth muscle cells with a particularly high density in

e
the branches of arteries (c alled arterioles). The smooth muscle cells are circular

(rather than radial or longitudinal) so when they contract, the diameter of the

r
lumen is narrowed. This is c alled vasoconstriction and it reduces ow of blood

along an artery or arteriole. When the smooth muscle cells relax, the lumen

y
widens and blood ow is increased. This is vasodilation. The smooth muscle cells

respond to hormone and neural signals and enable the body to adjust the ow

l
rate of blood to tissues in each organ depending on availability and need.

n
t
ATL Communic ation skills: Drawing plan diagrams

O
i
A plan diagram is a drawing that shows the distribution of join up lines

s
use a sharp pencil draw lines freehand,

tissues in an organ. It does not show individual cells. E ach carefully to

with a hard lead to but use a ruler for

r
line on the drawing represents the interface between form continuous

y
draw single sharp labelling lines

two tissues. The low power objective of a microscope structures such as

lines
e
cells
is usually used to observe the distribution of tissues, so

p
cell cell

that a plan diagram c an be drawn. Unnecessary detail is

v

avoided and if any of the areas of tissue are shaded, this

is done very faintly. Everything on the drawing should be

o
i

bad good bad good bad good

shown to the same magnic ation.

n

▴ Figure 6 Good and bad plan diagrams

U

B3.2.4 Measurement of pulse rates

Every time the heart beats, a wave of blood under high pressure passes along the
o
d

arteries. Where an artery is close to the body surface, this pressure wave c an be

felt as a pulse. This is bec ause the artery wall becomes stretched and then recoils.
i
r

There is one pulse per beat of the heart, so measurement of pulse rate allows
t

heart rate to be deduced. Pulse and heart rate are counted in beats per minute.
o

The wrist and the neck are two parts of the body where the pulse c an oen be
f

felt. Two or three ngertips are pressed lightly against the skin where the artery
u
x

is loc ated. The thumb should not be used bec ause it has a pulse which could

c auseconfusion.
l
O

a
v

▸ Figure 7 The radial pulse is on the

thumb side of the wrist. There is a c arotid

E

pulse on either side of your neck in the

groove next to the windpipe. Counts c an be

done for a whole minute or for 30 seconds

and then doubled

274
 Organisms

It is also possible to use digital meters to c alculate pulse rate. Pulse oximeters

are usually clipped to a ngertip. They have LEDs that shine red and infrared

light through the nger and detectors to measure how much of the light passes

through the tissues of the nger. This enables detection of variation in the amount

of blood in the tissues each time the heart beats, and from this the heart rate

s
is c alculated. The percentage saturation of the blood with oxygen c an also be

deduced bec ause deoxygenated blood absorbs red light whereas oxygenated

s
blood absorbs infrared light.

e
r
Assessing reliability and accuracy of tools:

P
Traditional versus digital estimation of heart rate

y
Try the traditional method of estimating heart rate by measuring pulse rate and

l
y
also the more modern approach of using a pulse oximeter.

n
• Do you get the same estimates for your heart rate?

O
Devise a procedure for assessing the reliability and accuracy of the traditional

i
and modern methods.

s
• Which method is more reliable?

y
e

p
B3.2.5 Adaptations of veins for the return of

▴ Figure 8 Varicose veins develop in the

v

blood to the heart legs when pocket valves become weakened

o or damaged. Blood can then ow backwards

i

Veins collect blood from all organs of the body and convey it back to the heart.

in the vein and accumulate, causing swelling

n

Blood drains out of c apillaries into veins continuously. This means there is no

and enlargement. Varicose veins usually

pulse. The wall of a vein contains far fewer elastic bres than the wall of an artery.

develop in the legs because venous return to

There are also far fewer smooth muscle cells bec ause veins are not used to adjust
U

the heart is usually againstgravity

blood ows to dierent parts of the body.

n

Blood in veins is at much lower pressure than in arteries, so the wall does not
o

need to be thick to prevent bursting. The potential problem from the low blood
d

pressure in a vein is backow towards the c apillaries and insucient return of

i

blood to the heart. To maintain circulation, veins contain pocket valves. These
r

consist of three cup-shaped aps of tissue projecting into the vein in the direction
t
o

of blood ow.
a

• If blood starts to flow backwards, it gets c aught in the flaps of the pocket
f

valve, which fill with blood and close the valve. This blocks the lumen of
x

thevein.
l

• When blood flows towards the heart, it pushes the flaps to the sides of the
O

vein. The pocket valve therefore opens and blood c an flow freely.

Blood ow in veins is assisted by gravity and by pressures exerted by adjacent

v

tissues, especially skeletal muscles. Contraction makes a muscle shorter and

wider so it squeezes on adjacent veins like a pump. The relatively thin walls of
E

veins help bec ause they allow a vein to be squeezed into a atter shape. Walking,

sitting or even just dgeting greatly improves venous blood ow. Around

80% of the blood in a person at rest is in the veins, but this is reduced during
▴ Figure 9 Discuss the pattern of venous

vigorousexercise. return that is occurring in the gymnast

during this manoeuvre

275
 Form and function

Standing on your head

Pocket valves and vein walls become less ecient with age, c ausing poor

venous return to the heart. Have you ever performed gymnastic moves such

s
as headstands or handstands, or experienced very high g-forces on a ride

at an amusement park? Young people c an mostly do any of these activities

s
▾ Figure 10 A normal artery (top) has a

easily but older people may not be able to. What is the explanation?

much wider lumen than an artery that is

e
occluded by atheroma (bottom)

r
B3.2.6 C auses and consequences of

P
occlusion of the coronary arteries

y
The aorta c arries blood pumped by the le side of the heart to all organs of

l
the body apart from the lungs. Two arteries branch o from the aorta close to

n
its origin at the semilunar valve. They are the right coronary artery that supplies

the right side of the heart and the le coronary artery, which branches into two

O
arteries that supply the le anterior and le posterior regions of the heart wall.

i
There are thus three main coronary arteries, each of which branches repeatedly

s
to provide oxygenated blood to all parts of the muscular wall of the heart.

y
The coronary arteries c an become narrowed or totally blocked by fatty

deposits. The fatty deposits are c alled atheroma (plaque) and the blockage
e

p
is an occlusion. The deposits build up in the wall of the artery and contain

a variety of lipids including cholesterol. They restrict blood ow to the

v

downstre am region of the he art wall, oen c ausing pain in the chest (angina)

o
i

or shortness of bre ath, especially during exercise.

n

F atty deposits in the artery wall c an become impregnated with c alcium salts,

which harden the artery and make the inner surface rough. This tends to trigger
U

the formation of a blood clot (thrombosis). Hypertension (high blood pressure)

n

increases the risk of thrombosis. Blood clots c an block the ow of blood to part

of the muscular wall of the heart, depriving it of oxygen and preventing normal

contractions. This is known as a heart attack.

o
d

aorta le and right

i
r

carotid arteries

right pulmonary
t

(used for taking

o

vein (red indicates

a

a pulse)

oxygenated blood)
f

le coronary
right pulmonary
x

artery
artery (blue indicates
l

deoxygenated blood)
O

le anterior

descending
v

right
coronary artery

coronary
(a branch of the
E

artery
le coronary

artery)

▴ Figure 11 The coronary arteries are the rst branches o the aorta

276
 Organisms

If a blockage persists there will be tissue death and therefore permanent damage

to the heart. Tissue death in heart muscle due to inadequate blood supply is called

a myocardial infarction. The conditions associated with narrowed or blocked

coronary arteries are collectively known as coronary heart disease(CHD).

s
Coronary heart disease is very common and there have been many

epidemiologic al studies to try to identify risk factors and c auses. Epidemiology is

s
the study of nature and spread of diseases in the human population. Multiple risk

e
factors have been identied:

• hypertension — raised blood pressure increases the chance of blood

r
clotformation

y
• smoking — raises blood pressure bec ause nicotine c auses vasoconstriction

• eating too much saturated fat and cholesterol — promotes plaque formation

l
• obesity — associated with raised blood pressure and high blood cholesterol

n
concentrations

t
• high salt intake — a large quantity of sodium chloride in the diet raises

O
i
bloodpressure

s
• drinking excessive amounts of alcohol — associated with raised blood

pressure and obesity

y
• sedentary lifestyles — a lack of exercise is correlated with obesity and prevents
e
the return of venous blood from the extremities leading to a greater risk of

p
clot formation
v

• genetic predisposition — some genes increase the risk of hypertension

andthrombosis
o
i
n

• old age — blood vessels become less flexible.

U

Data-based questions: Hypertension

n

Hypertension is a major risk factor for coronary heart 4. Evaluate the impact of differences between
o
d

diseases. In a major study, more than 316,000 males systolicand diastolic pressure on death rate. [3]

were followed for 12 years to investigate the eects of

81
i
r

high blood pressure. Figure 12 shows the relationship

t

between systolic and diastolic blood pressure and the

coronary art
o

43

eect on the death rate per 10,000 people per year.

disas dat rat / 44
a

37
35 36
1
Systolic pressure is the maximum pressure reached in
10000 rsons yar
f

32
arteries aer the ventricles have contracted. Diastolic
u

26
25
25
25
x

25
pressure is the minimum pressure in the arteries just

24

before the ventricles contract again. >160

17
l

14
13
O

13
12
21 140–159
a

1. Determine the death rate for a systolic blood

10
pressurebetween 140 mmHg and 159 mmHg 12
120–139
9
9
9
v

anda diastolic blood pressure between

systolic BP /
<120
0
75 mmHg and 79 mmHg. [1] 0 9
1 9
> – 9
0 8 9 mm
9 – 7
0 – 4
7 0
E

8 5 –
7 7
0 <
7
2. Describe the effect of systolic blood pressure Hg

diastolic BP / mmHg
anddiastolic blood pressure on the death rate. [2]

▴ Figure 12 The eect of blood pressure on coronary heart

3. C alculate the minimum difference between

disease
systolicand diastolic blood pressure where

thedeathrate is highest. [1]

277
 Form and function

Patterns and trends: Correlation coecients

A correlation is an association between two numerical A correlation coecient is a numeric al measure of the

variables. For example, we might expect a correlation level of association between two variables. It provides an

s
between wingspan and body mass in blue jays (Cyanocitta objective assessment of the strength of the correlation. If

cristata) or between average saturated fat intake per the points on a sc atter diagram lie exactly on a straight line

s
person and CHD rate of dierent countries. Two variables with positive gradient, the correlation coecient is 1. If the

e
are positively correlated if higher values of one variable points lie exactly on a straight line with negative gradient,

tend to correspond to higher values of the other variable. the correlation coecient is −1. If there is no correlation,

r
The variables are negatively correlated if higher values the correlation coecient is 0. For most relationships, the

of one variable tend to correspond to lower values of correlation coecient is somewhere between 1 and −1.

y
the other variable. If there is no relationship between the

These numeric al measures of correlation are used in

variables, they are uncorrelated or independent

l
testing hypotheses. High correlation coecients c an

y
D ata c an be displayed in a sc atter diagram to show the provide signic ant evidence of association between two

n
extent to which two variables are correlated. If the points factors, for example mean intake of saturated fatty acids

t
are fairly widely sc attered, there is weak correlation. If per person and CHD rate of dierent countries. However,

O
the variables lie very close to a straight line with positive even a strong correlation such as this one does not prove

i
gradient there is strong positive correlation. If the a c ausal link. Scientic and medic al research is needed to

s
variables lie very close to a straight line with negative establish a biologic al mechanism by which saturated fat

r
gradient, there is strong negative correlation. A sc atter intake causes increased risk of CHD. However, the time

y
diagram only shows a sample taken from the whole and expense involved in nding such a mechanism would
e

p
population, and with a small sample it is usually hard to not be invested in unless a high correlation had been

reach conclusions about the whole population. established rst.

v

o
i
n

B3.2.7 Transport of water from roots to

U

leaves during transpiration

n

Xylem is the tissue in plants that is used to transport water. Water is absorbed by

roots and lost from leaves in transpiration, so the main ow of water is from the
o
d

roots to the leaves. If suction is applied to the top of an air-lled tube with its base

in water, the water is eectively pushed up the tube by atmospheric pressure and
i

reaches a maximum height of 10.4 m. Trees c an grow to more than 10 times this
r

height and water ows to the top of them, so the mechanism used in plants must
t
o

be dierent from just atmospheric pressure.

a

Xylem vessels are normally lled by xylem sap, which consists of water with
f

relatively low concentrations of potassium, chloride and other ions. In a transpiring

x

leaf, water is lost by evaporation from the cell walls of spongy mesophyll cells
l

and then diusion of water vapour out through the stomata. Cell walls contain a
O

mesh of cellulose molecules which are hydrophilic and form hydrogen bonds with

water. There is adhesion between the water and the cellulose of the cell walls. Loss
v

of water therefore causes water to be drawn through the interconnected leaf cell

walls in the pores between cellulose molecules. This process is a type of capillary
E

action and is similar to the way that water is drawn through lter paper (also mostly

composed of cellulose). The source of the water that is drawn through leaf cell

walls is a xylem vessel in the nearest vein.

278
 Organisms

As the cell walls of leaf cells draw out water from xylem, they generate tensions

(pulling forces). As long as there is a continuous column of water in a xylem vessel,

these tensions are transmitted from the leaves down to the roots. This is called

transpiration pull and is strong enough to move water upwards, against the force

of gravity, to the top of the tallest tree. For the plant, it is a passive process; all the

s
energy needed comes from the thermal energy (heat) that causes transpiration.

s
The pulling of water upwards in xylem vessels depends on the cohesion that

e
exists between water molecules. M any liquids would be unable to resist the

very low pressures in xylem vessels and the column of liquid would break. This

r
is c alled c avitation and it does occ asionally happen even with water, but it is

unusual. Even though water is a liquid, it c an transmit pulling forces in the same

y
way that a solid length of rope does.

l
lignified thickening

y
cellulose Key

n
of xylem vessel wall
cell walls
capillary

t
action in

O
cell walls
llyhposem ygnops

i
evaporation

s
from cell walls

r
diffusion

y
through air
e
spaces and

p
out through
v

stomata

o
i

lower

waxy
n

epidermis

cuticle
with stoma
U

▴ Figure 13 Water movements in the leaf

o
d

Modelling water movement through cell walls

i
r

• How high do you expect water to rise in the

strips of
t
o

papertowel?
paper towel
a

• Do you expect any difference between the

f

stoppered and unstoppered tubes?

u
x

• What other factors could be varied?

l

Test your hypotheses by setting up experiments.

O

• How does this model help us to understand water

water (to which

movement in plants?
◂ Figure 14 Tall tubes
v

dye could be
with paper towel strips

added)
dipping into water, one
E

sealed and one open to

the air

279
 Form and function

B3.2.8 Adaptations of xylem vessels for

transport of water

The structure of xylem vessels allows them to transport water inside plants very

eciently. They are formed from columns of cells, arranged end-to-end. The cell wall

s
material between adjacent cells in the column is largely removed and the plasma

s
membranes and contents of the cells break down. This creates long continuous

tubes, with minimal resistance to the ow of xylem sap. When mature, xylem vessels

e
are non-living, so the ow of water along them must be a passiveprocess.

r
The vessel walls are thickened, and the thickenings are impregnated with a

P
polymer c alled lignin. The pressure inside xylem vessels is usually much lower

y
than atmospheric pressure and there is commonly tension (negative pressure

potential) but the strength of the walls prevents the xylem vessel from collapsing.

l
y

n
The lignied wall thickenings are impermeable to water but there are always gaps

in the thickening through which water c an enter and exit. In the xylem vessels

O
formed by young plants, the wall thickenings are in rings or helices with large

i
gaps for water passage. In older plants, the wall thickenings are more extensive,

s
with holes c alled pits through which water c an pass.

r
▴ Figure 15 Light micrograph of a vertic al

y
thickenings of
section of the primary wood or xylem of a
e
tree showing wood vessels with lignied xylem vessel wall

p
supporting thickenings impregnated
v

with lignin

o
i
n

C
U

n
o
d

pits
i
r

t
o

wall
f

of xylem
u
x

vessel
l

continuous tubular
O

structure
▴ Figure 16 Longitudinal section through

a rhubarb stem, Rheum rhaponticum. Cut

▴ Figure 17 Structure of xylem vessels ▴ Figure 18 Structure of xylem vessels in

v

xylem vessels are coloured brown. Xylem

in growing parts of the plant such as roots parts of the plant that are thickening such as

vessels are reinforced and strengthened

andstems the trunk or roots of a tree

E

with spiral bands of lignin. Spiral bands

allow xylem vessels to elongate and

growlengthwise and also retain their

exibility

280
 Organisms

B3.2.9 Distribution of tissues in a transverse

section of the stem of a dicotyledonous plant

The outer layer of cells in all parts of a young plant is the epidermis. The stems of

dicotyledonous plants (dicots) typic ally have transport tissue in vascular bundles

s
near the epidermis. Dicots have two seed leaves and include sunowers, peas

s
and oaks and most other owering plants. The xylem is usually on the inner side

of a vascular bundle and the phloem on the outer side, with c ambium consisting

e
of stem cells between. The other tissues that usually occur in a dicot stem are pith

in the centre and cortex near the epidermis.

r
P

y
▾ Table 2 Plant tissues and their functions

Tissue M ain functions in stems

l
epidermis

y
xylem

n
Xylem Transport of water from roots to leaves

vascular

t
Phloem Transport of sugars from leaves to roots cambium

cortex bundle

O
i
C ambium Production of more xylem and phloem
phloem

s
Epidermis Waterproong and protection

pith

r
Cortex Support and photosynthesis

y
e
Pith Bulking out the stem
▴ Figure 19 Tissue plan of a stem in a typic al dicotyledonous plant

p
v

Applic ation of skills: Drawing stem tissue plans

o
i
n

Full instructions for drawing tissue plans are given in

Section B3.1.8. The arrangement of tissues is not the same

sclerenchyma
U

in all plant stems, so it is essential either to view a stem

bres (crimson)

section with a microscope while drawing a plan, or view a

n

micrograph, such as that in Figure 20.

o

There are many variations in stem structure. Some dicots

d

such as elder (Sambucus nigra) have a hollow centre to

i

the stem instead of pith. Some dicots such as cucumber phloem

r

(dark blue)
(Cucumis sativa) have two areas of phloem in each
t
o

vascular bundle, instead of just one. Some dicots such as

a

sunowers (Helianthus annuus) have sclerenchyma tissue

f

(bres) adjacent to each vascular bundle. These variations

u

in stem structure c an be shown by drawing tissue plans.

x

c ambium

Figure 20 is a micrograph showing one vascular bundle in

(light blue)
l

part of a young sunower stem. Draw a tissue plan based

O

on this micrograph.

xylem
v

(red)
E

▴ Figure 20 Light micrograph of a section through a young stem

from a sunower (Helianthus annuus), showing one of the many

vascular bundles

281
 Form and function

B3.2.10 Distribution of tissues in a transverse

section of the root of a dicotyledonous plant

The distribution of tissues in stems and roots of dicotyledonous plants is dierent.

All the vascular tissue is grouped in the centre of a root, with xylem in a star-

s
shaped area and phloem between the points of the star. The xylem vessels c an

s
be identied by their large size, thick walls and rounded shape in transverse

section. Xylem walls may be stained red in microscope images bec ause they

e
are lignied. Other cells in the root are unlignied and are usually stained blue.

Phloem cells are smaller than xylem with thinner walls. The outer layer of cells

r
in the root is epidermis, with small cells that may have root hairs protruding.

y
Between the vascular tissue and the epidermis there is cortex, with relatively large

and thin-walled cells.

l
y

n
epidermi s

Applic ation of skills:

—absorbs water and mineral ions

t
from the soil oen using long
Drawing root tissue

O
xylem
narrow outgrowths (root hairs)

i
plans —transports

s
water from

Figure 22 shows part of a root of the roots up

y
Allium tuberosum in transverse to the stem and
e
section. Draw a tissue plan to leaves

p
identify the tissues.
v

o
i

phloem
n

—transports

sucrose from

the leaves to
U

the roots
endodermis
n

—an inner skin of cells that

cortex

water must pass through to

o

—unspecialized cells
d

reach the xylem

that bulk out the root to

strengthen it and increase

i
r

its surface area

t
o

▴
a

Figure 21 Tissue plan of a dicot root

f

u
x

l
O

▴ Figure 22
v
E

282
 Organisms

LHA
B3.2.11 Release and reuptake of tissue uid

in c apillaries

Plasma is the uid in which the blood cells are suspended. It consists of water

with many dierent dissolved substances: glucose, amino acids, mineral ions

s
such as chloride and sodium, vitamins, hormones and plasma proteins. Lipids

s
are c arried in lipoprotein droplets. The structure of the c apillary wall (described
blood plasma cerebrospinal

inSection B3.2.1) is adapted to let part of the blood plasma leak out into spaces
(7%) fluid (1%)

e
between the cells in a tissue. Most protein molecules are too large to pass

through the basement membrane so are retained in the plasma, but other

r
substances c an pass out through the c apillary wall.

tissue fluid

y
intracellular

(26%)
The uid that leaks out of c apillaries is a type of extracellular uid, c alled tissue

fluid (67%)
3

uid. At any time, there are about 14 dm of this tissue uid in the tissues of a

l
70 kg human, so it constitutes about 20% of body mass. There is a continual

n
process of release and reuptake of tissue uid. C apillaries that are close to an

t
arteriole tend to release tissue uid bec ause the blood supplied by the arteriole

O
is at high pressure. Reuptake tends to happen in c apillaries that are close to a

i
▴ Figure 23 Distribution of water in the

venule, where the blood pressure is much lower.

human body

s
r

y
B3.2.12 Exchange of substances between
e

p
tissue uid and cells in tissues
v

Tissue uid contains oxygen, glucose and all other substances in blood plasma

apart from large protein molecules, which c annot pass through the c apillary wall.
o
i

The uid ows between the cells in a tissue, allowing the cells to absorb useful
n

substances. Oxygen is absorbed from the tissue uid by diusion bec ause the

oxygen concentration in cells is lower due to aerobic respiration. Glucose, also

U

used in aerobic respiration, is absorbed by sodium–glucose cotransporters.

n

Growing cells absorb amino acids by active transport.

C arbon dioxide, produced by cell respiration, diuses out of cells into the
o
d

tissue uid, along with other waste products of metabolism. As tissue uid ows

between the cells of a tissue it accumulates dissolved waste products. The tissue
i
r

uid then re-enters the c apillary network, becoming part of the blood plasma.
t

The c apillaries merge to form venules, which c arry the waste products out of the
o

tissue. C arbon dioxide is excreted by the lungs and other waste products are

detoxied by the liver or excreted by the kidneys.

f

u
x

release of reuptake of

oxygenated blood tissue fluid deoxygenated blood

tissue fluid
l

entering capillaries exiting capillaries

O

a
v
E

oxygen absorption
carbon dioxide excretion

by respiring cells
from respiring cells

▴ Figure 24 Exchange processes in respiring tissues 283

 Form and function
LHA

B3.2.13 Drainage of excess tissue uid into

lymph ducts

Most of the tissue uid released by c apillaries returns to them, but some does

not. Of the 20 dm of tissue uid produced per day in an average adult’s body,

s
3 3

17dm return to the c apillaries. If the other 3 dm of uid stayed in tissues it

s
would c ause swelling, c alled oedema. This is prevented by the drainage of tissue

uid into vessels of the lymphatic system.

e
r
wall of lymphatic vessel composed

of a single layer of endothelium cells basement membrane

y
with pores between with large gaps

l
y

n
t

O
i
s
r

y
e

p
v

o
i
n

C
U

lymph
anchoring filaments

tissue cells
o
d

▴ Figure 25 Narrow ending of a lymph vessel into which excess tissue uid drains
i
r

In all tissues, there are narrow blind-ended lymphatic vessels with permeable
t

walls through which tissue uid c an pass. Aer entering the lymphatic vessels,
o

the uid is known as lymph rather than tissue uid. The narrow vessels join up
a

repeatedly to form wider lymphatic vessels. At the end of this system of vessels,
f

there are just two — the le and right lymphatic ducts. These merge with the
x

subclavian veins. Lymph is therefore drained o from all tissues of the body and

is returned to the blood system. Blood in the subclavian veins ows into the vena
l
O

c ava and on to the right side of the heart.

a
v

B3.2.14 Dierences between the single

E

circulation of bony sh and the double

circulation of mammals

There are valves in mammalian veins and heart that ensure a one-way ow, so

blood circulates through arteries, c apillaries and veins. M ammals pump blood

to the lungs to be oxygenated. The blood must be at relatively low pressure to

284
 Organisms

LHA
prevent c apillaries in the alveoli from bursting. Aer owing through the alveolar

c apillaries, the residual pressure is too low for the blood to ow on to other lungs

organs of the body, so it returns to the heart to be re-pumped. Oxygenated

blood returning from the lungs must not mix with deoxygenated blood being
pulmonary

pumped to the lungs, so the heart has separate le and right sides. circulation

s
The le side of the heart receives oxygenated blood and pumps it to all

s
organs of the body apart from the lungs. This requires relatively high blood

e
pressure. The kidneys in particular c arry out pressure ltration of blood, so need

much higher blood pressure than the lungs. With a few notable exceptions,

r
oxygenated blood pumped by the le side of the heart ows through c apillaries

in only one organ of the body and then returns to the heart deoxygenated and

y
at much lower pressure. It returns to the right side of the heart, which pumps

blood to the lungs.

heart

l
y
M ammals have a double circulation, with the blood passing twice through the

n
heart to make a full circuit. The heart is a double pump, delivering blood under

t
dierent pressures to dierent organs of the body. The two circulations are

O
known as the pulmonary and systemic circulations. The pulmonary circulation

i
systemic circulation
receives deoxygenated blood that has returned from the systemic circulation,

s
and the systemic circulation receives blood that has been oxygenated by the

other

r
pulmonary circulation.

y
organs
e
Fish pump blood to their gills to be oxygenated. The blood ows through

p
c apillaries in narrow gill laments. Water is pumped over the gill laments and ▴ Figure 26 The double circulation of
v

mammals
oxygen diuses from water to the blood; c arbon dioxide moves in the opposite

direction. The blood c an be pumped at high pressure to the gills bec ause the

o
i

surrounding water provides support and reduces the risk of c apillaries bursting.
n

Aer owing through the gills, the blood is oxygenated and still has enough

pressure to ow directly to another organ of the body. While passing through
U

c apillaries in one organ, the blood becomes deoxygenated and its pressure
n

falls, so it must return to the heart for re-pumping to the gills. Fish thus have a

singlecirculation.
o
d

heart
i
r

afferent arteries
t
o

veins
a
f

u
x

l
O

gills
v

other organs
E

efferent arteries

▴ Figure 27 The single circulation of sh

285
 Form and function
LHA

B3.2.15 Adaptations of the mammalian heart

for delivering pressurized blood to the arteries

The mammalian heart has evolved to pump pressurized blood to the organs of

the body continuously throughout our lives. It is well adapted through its form to

s
c arry out this function.

s
• Ventricles — chambers with a strong muscular wall that c an generate high

e
blood pressure when it contracts, pumping blood out into the arteries.

• Atria — chambers with a thinner muscular wall that collect blood from the

r
veins and pump it on to the ventricle, so the ventricle is as full as possible

P
when it contracts and the atrium is as empty as possible so it c an collect more

y
blood from the veins.

l
• Atrioventricular valves between the atria and the ventricles. These valves

n
close to prevent backflow of blood to the atria when the ventricles contract

and open to allow blood to flow from the atria to the ventricles when the

t
ventricles relax.

O
i
• Semilunar valves between the ventricle and the artery. These valves close

s
to prevent backflow of blood to the ventricles when the ventricles relax and

open to allow blood to flow from the ventricles to the arteries when the

y
ventricles contract.
e
• C ardiac muscle — specialized muscle tissue that forms the wall of the

p
ventricles and atria. C ardiac muscle has branched cells and connections
v

between plasma membranes of adjacent cells that allow electric al signals to

be propagated throughout the wall of

othe heart. This enables coordinated
i

contractions. C ardiac muscle is unique in the body bec ause it c an contract

n

without stimulation from motor neurons. The contraction is c alled myogenic;

this means that it is generated in the muscle itself. The membrane of a heart
U

muscle cell depolarizes when the cell contracts and this activates adjacent
n

cells, so they also contract. A group of cells therefore contracts almost

simultaneously at the rate of the fastest.

o
d

c arotid
i
r

arteries
t

aorta
vena
o

c ava

pulmonary

artery
f

right
x

atrium le

atrium
l
O

a
v
E

right le

ventricle ventricle

▴ Figure 28 Exterior view of the heart in its position in the thorax

286
 Organisms

LHA
• Pacemaker — the sinoatrial node in the wall of the semilunar valve aorta

right atrium initiates each heartbeat by sending

pulmonary artery

an electric al signal into the atria. The interval

between signals determines the rate (pace) of

vena cavae

the heartbeat. The sinoatrial node is the region pulmonary veins

s
of the heart with the fastest rate of spontaneous

beating. The cells of the sinoatrial node have few

s
of the proteins that c ause contraction in other

e
muscle cells, but they have extensive membranes.

The sinoatrial node c an initiate each heartbeat

r
bec ause the membranes of its cells are the first to

depolarize in each c ardiac cycle.

y
semilunar

• Septum — the wall of the heart between the left

valve

l
and right ventricles and between the left and right

y
atria. It prevents oxygenated blood in the left

n
side of the heart from mixing with deoxygenated

t
blood in the right side.

O
i
• Coronary vessels — coronary arteries and veins

s
in the wall of the heart. Coronary arteries c arry

oxygenated blood from the aorta to all parts of

y
atrioventricular
the heart wall, supplying oxygen and glucose.

right atrium

valves
e
Coronary veins collect deoxygenated blood from

p
the heart wall and return it to the right atrium.
v

right ventricle le ventricle

o septum
i

▴
n

Figure 29 Structure of the heart

U

Structure and function of the heart

n

Discuss the answers to these questions. 4. Does the left side of the heart pump oxygenated or
o

deoxygenated blood?
d

1. How do you explain the walls of the atria being

5. Why does the wall of the heart need its own supply of
thinner than the walls of the ventricles?
i
r

blood, brought by the coronary arteries?

2. What prevents the atrioventricular valve from being

t

6. Does the right side of the heart pump a greater

o

pushed into the atrium when the ventricle contracts?

a

volume of blood per minute, a smaller volume per

3. How do you explain the left ventricle wall being

minute, or the same volume per minute as the left?

f

thicker than the right ventricle wall?

u
x

l
O

B3.2.16 Stages in the c ardiac cycle

v

The heart follows a repeating sequence of actions, known as the c ardiac cycle.

The sinoatrial node initiates each turn of the cycle by sending out an electric al
E

signal that spreads throughout the walls of the atria. It takes less than a 10th

of a second for all cells in the atria to receive the signal. This propagation of

the electric al signal c auses the whole of both le and right atria to contract.

Aer a time-delay of about 0.1 seconds, the electric al signal is conveyed to the

ventricles. The delay allows the atria to pump the blood that they are holding into

the ventricles. The electric al signal is then propagated throughout the walls of the

ventricles, stimulating them to contract and pump blood out into the arteries.

287
 Form and function
LHA

Stages in the c ardiac cycle c an be deduced from a graph showing pressure

changes during a heartbeat in the atrium, ventricle and artery on one side of the

heart. Figure 30 shows the state of heart chambers and valves during the stages

of a heartbeat. Vertic al arrows show ows of blood.

s
vein

s
3 3
atrium 25 cm 45 cm

atrium
atrium relaxing atrium relaxing

e
contracts

3
atrioventricular valve atrioventricular valve
25 cm

atrioventricular valve

r
valve open
closed open

P
ventricle ventricle

y
ventricle ventricle relaxing

relaxing contracting 3
0 cm

l
3
semilunar valve 80 cm semilunar valve closed

n
artery diastolic systolic diastolic

O
i
tissues of the body

s
0 0.1 0.15 0.4 0.45 0.8

r
time / s

y
▴ Figure 30 Summary of stages of the c ardiac cycle with arrows to indic ate blood ow between the vein, atrium, ventricle and artery,
e

p
including typic al volumes
v

0.0–0.1 seconds: atrial systole

The atrium contracts causing a

o
rapid but relatively small
i

pressure increase, which pumps blood from the atrium to

n

the ventricle, through the open atrioventricular valve.

The semilunar valve is closed and blood pressure in the

U

artery gradually drops to its minimum as blood flow

n

continues along it and no blood is being pumped in from

the artery.
o
d

i
r

0.45–0.8 seconds: ventricular diastole 0.1–0.15 seconds: ventricular systole

t
o

Pressure in the ventricle drops below the The ventricle contracts, with a rapid pressure build-
a

pressure in the atrium so the atrioventricular up that causes the atrioventricular valve to close.
f

valve opens.
u

The semilunar valve remains closed.

Blood from the vein drains into the atrium

x

and from there into the ventricle, causing a

l

slow increase in pressure.

O

a
v
E

0.4–0.45 seconds: ventricular diastole 0.15–0.4 seconds: ventricular systole

The ventricle stops contracting and The pressure in the ventricle rises above the pressure

pressure inside it rapidly drops below the in the artery so the semilunar valve opens and blood is

pressure in the artery, causing the semilunar pumped from the ventricle into the artery, maximizing
▸ Figure

valve to close. the arterial blood pressure.

31 Timing of

The atrioventricular valve remains closed. Pressure slowly rises in the atrium as blood drains in
actions in the

from the vein and the atrium fills.

c ardiac cycle

288
 Organisms

LHA
Data-based questions: Heart action and blood pressures

Figure 32 shows the pressures in the atrium, ventricle and

artery on one side of the heart, during one second in the ventricle

120

s
life of the heart.

1. Deduce when blood is being pumped from the

s
artery

100
atrium to the ventricle. Give both the start and the

e
end times. [2]

80
2. Deduce when the ventricle starts to contract. [1]

r
gH mm / erusserp
3. The atrioventricular valve is the valve between

y
the atrium and the ventricle. State when the 60

atrioventricular valve closes. [1]

l
4. The semilunar valve is the valve between the

y
40

n
ventricle and the artery. State when the semilunar

t
valve opens. [1]

O
20
atrium

i
5. Deduce when the semilunar valve closes. [1]

s
6. Deduce when blood is being pumped from the

ventricle to the artery. Give both the start and the

y
endtimes. [2] e
–20

7. Deduce when the volume of blood in the ventricle is:

p
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8

a. at a maximum [1]
v

time / s
b. at a minimum. [1]

o
i

▴ Figure 32 Pressure changes in the atrium and ventricle of the

heart and the aorta during a c ardiac cycle. The timings assume a
n

heart rate of 75 beats per minute

U

B3.2.17 Generation of root pressure in xylem

o
d

vessels by active transport of mineralions

Water has to pass through at least one root cell before it enters a xylem vessel. If
i
r

the plant is transpiring, xylem vessels will be lled with sap that is under tension.
t

The tension is strong enough to draw water out of root cells and into xylem
o

vessels, even though the xylem sap is hypotonic to root cells and water might

be expected to move in the opposite direction by osmosis. If the plant is not

f

transpiring, there is likely to be positive pressure rather than tension in the sap
x

and another mechanism is needed to c ause water to move into xylem vessels
l

from root cells.

O

There are various reasons for transpiration not occurring.

v

• High atmospheric humidity may prevent diffusion of water vapour through

stomata from air spaces inside the leaf to the atmosphere outside.
E

• At night, most plants close their stomata, preventing transpiration and in

some c ases allowing xylem vessels to become air-filled as the sap sinks back

down to the roots. ▴ Figure 33 If grape vines are pruned

too late in winter when sap has started

• In deciduous trees that have been leafless in winter, xylem vessels are air-

to rise due to root pressure, there c an be

filled but must become refilled with sap before new leaves have grown and

“bleeding” of sap from the cut ends of

started transpiring in spring.

thestems

289
 Form and function
LHA

water Root pressure is the mechanism that is used to

transport of ions
movement by rell xylem vessels with sap when they have been

such as potassium
osmosis air-lled. It also c auses sap to rise when the xylem

sap is not under tension. Root cells adjacent to

xylem vessels load mineral ions into the vessels by

s
active transport. The pump proteins that c arry out

plasma membrane active transport are in the plasma membranes of

s
with pump proteins these living cells. The xylem vessels are dead and

e
for active transport of do not have plasma membranes. Active transport

ions into xylem vessels makes the xylem sap hypertonic compared with

r
the cytoplasm of the adjacent cells, so water moves

from them to the xylem vessels by osmosis. This

y
raises the pressure inside the vessels and pushes

the sap upwards, against the force of gravity. Unlike

l
pumps that c ause uids to rise by creating a vacuum

n
above them, root pressure is not dependent on

atmospheric pressure so there is no limit to the

O
height to which xylem sapc anrise.

i
wall thickenings that

are impermeable to

s
water and ions so

r
prevent leakage from

y
xylem vessels when
e
there is root pressure

p
v

o
cortex endodermis xylem
i

cells vessel
n

▴ Figure 34 Generation of root pressure by active

transport of ions and water movement by osmosis

U

Data-based questions: Modelling root pressure

o
d

Water moves from an area of higher water potential to 1. C alculate the water potential of the soil and the

an area of lower water potential. The contributions of xylemsap. [2]

i
r

solute potential (Ψ ) and pressure potential (Ψ ) to water

t

s P
2. Deduce the direction of water movement between
o

potential (Ψ ) are described in Section D2.3.10

W
the soil, the cytoplasm of root cells and the xylem
a

sap. Give reasons for your answer. [3]

Table 3 shows a model scenario for generating root

f

pressure by active transport of ions and water movement 3. The solute potentials are due almost entirely to
x

by osmosis. dissolved ions. Deduce, giving a reason for your

l

answer, how ions are moved from the cytoplasm

O

compartment Ψ /kPa Ψ /kPa Ψ /kPa

P s W
ofroot cells to the xylem sap. [2]
a

soil 0 −250

4. State what is indic ated by a pressure potential of

v

cytoplasm of root cells 300 −650 −350 zeroin the soil. [1]

5. Discuss the reasons for the difference in pressure

xylem sap 100 −750
E

potential between the cytoplasm of the root cells

▴ Table 3
andthe xylem sap. [2]

290
 Organisms

LHA
B3.2.18 Adaptations of phloem sieve tubes

and companion cells for transloc ation of sap

Sucrose and other c arbon compounds c an be transported from one part of a

plant to another. The transport is from sources to sinks. Sources are tissues of

s
the plant where the compounds are produced by photosynthesis or are being

s
unloaded from a store. Sinks are tissues that need to be supplied with substrates

for cell respiration or anabolic reactions as a part of growth or tissues where

e
starch or lipids are being stored. Leaves are sources bec ause they produce

c arbon compounds by photosynthesis. Roots are sinks bec ause they need

r
substrates for cell respiration.

y
Phloem is the tissue that transports c arbon compounds. Of the several cell types

within phloem, it is the sieve tubes that provide channels through which transport

l
c an occur. Sieve tubes develop from columns of cells. Adjacent cells in the

n
column become connected by large perforations (holes) in the end walls, which

t
are then c alled sieve plates. Nearly all the contents of the cells break down during

O
dierentiation, including the nucleus. The cell contents are replaced by phloem

i
sap, which is a solution of sucrose and other compounds being transported. The

s
loss of cell contents and the perforations of the end walls make it easier for the

r
sap to ow through the sieve tube.

y
e
It is debatable whether the remaining subunits of sieve tubes are still cells, but

p
they do have a membrane and use ATP for processes requiring energy, so they
v

are certainly alive. They are sometimes c alled sieve tube elements rather than

o
cells. The main energy-requiring process is loading and unloading sucrose,
i

which is c arried out by active transport. Sieve tube elements have few or no
n

mitochondria of their own and rely on adjacent companion cells for a supply.

▴ Figure 35 The holes in a c apsule used in

Companion cells have many mitochondria and ne cytoplasmic connections

a coee-making machine are reminiscent of

c alled plasmodesmata, through which the ATP c an pass. These plasmodesmata
U

the pores in a sieve plate

have a larger diameter than those elsewhere in the plant. In addition to ATP,
n

sucrose loaded into the companion cell by active transport c an pass through to

the sieve tube.

o
d

High solute concentrations develop in sieve tubes of the leaf and other sources.
i

This draws water in by osmosis, increasing the hydrostatic pressure. This could
r

not happen without the plasma membrane that is maintained in sieve tube
t
o

elements.
a

Although not as thick as in xylem, the cellulose cell walls of the sieve tube
f

elements c an withstand the high pressures that develop during transport. In

x

particular, the sieve plates brace the tube, preventing bulges or bursts.
l
O

Roots generally act as sinks bec ause they need substrates for cell respiration.
a

In roots and other sinks, compounds required by the tissue are unloaded by

active transport. This lowers the solute concentration in the sieve tubes, so
v

water exits by osmosis and the hydrostatic pressure drops. The dierence in

pressure between phloem sap in sources and sinks drives the ow of sap from
E

source to sink. Sieve tubes c an conduct sap in either direction (but not both

directions at once). As an example, sieve tubes transport c arbon compounds

into a growing leaf and then in the opposite direction out of the leaf when it is

producing morec arbon compounds by photosynthesis than it is using in growth

andrespiration.

291
 Form and function
LHA

phloem

sap

s
s
e
phloem sieve tube

element with

companion cell

r
plasma membrane

with nucleus,

(purple) but few or

mitochondria and

y
no organelles

other organelles

l
y

n
t

O
i
plasmodesmata

s
— tubes of plasma

membrane crossing the

y
cell walls to form a

sieve plate with pores through

cytoplasmic connection
▴ Figure 37 Freeze–fracture electron
e
which phloem sap can flow

p
micrograph showing cell walls in a

▴ Figure 36 Structure of a sieve tube element and adjacent companion cell sievetube
v

o
i
n

Linking questions

1. How do pressure dierences contribute to the movement ofmaterials in

U

an organism?
n

a. Describe the adaptations of arteries for high pressure transport of

blood away from the heart. (B3.2.3)

o
d

b. Explain the role of pressure ltration in the formation of tissue uid in

i
r

c apillaries. (B3.2.10)
t

c. Explain the role of the generation of root pressure in xylem vessels by

o

active transport of mineral ions. (B3.2.16)

f

2. What processes happen in cycles at each level of biologic al organization?

u
x

a. Compare and contrast cellular reproduction with the lysogenic cycle

of a virus. (A2.3.4)
l
O

b. O utline the stages of the c ardiac cycle. (B3.2.15)

c. Using examples, explain the role of oxidation and reduction in

v

biologic al systems. (B1.1.4)

E

292
B3.3 Muscle and motility

How do muscles contract and c ause movement?

s
s
The rowers in Figure 1 develop powerful muscles for use

in the power stroke, when the blade of the oar is pulled

e
through the water. The oar rests on a rowlock, which is

positioned 1 m from the end of a 3.7m racing oar. In which

r
direction will this boat move? In what ways is rowing a

y
good analogy for the mechanism within muscles that

c auses contraction and generation of force? Muscle tissue

l
is contractile—it c an shorten itself and exert a pulling force

n
as it does so. What is the relative role of actin and myosin in

muscle contraction?

O
i
s
r

y
▸ Figure 1
e

p
v

What are the benets to animals of having muscle tissue?

o
i

The golden silk orb-weaving spider (Nephila clavipes)

n

applies a potent neurotoxin to its web. Insects that

become c aught tremble and then move increasingly

U

slowly before becoming paralysed. The spider injects

n

enzymes and later sucks the digested contents out of the

insect’s exoskeleton. Without working muscle, the prey’s

survival chances are nil.

o
d

Which taxonomic group of animals lack muscle? What

i
r

role does muscle play in the organs of mammals such

t

as digestive systems or circulatory systems? What is the

o

role of skeletal muscle? How metabolic ally expensive is

a

muscle contraction?
f

▴ Figure 2 The golden silk orb-weaving spider (Nephila clavipes)

x

AHL only
l
O

B3.3.1 Adaptations for movement as a universal feature of living organisms

a

B3.3.2 Sliding lament model of muscle contraction

v

B3.3.3 Role of the protein titin and antagonistic muscles in muscle relaxation

B3.3.4 Structure and function of motor units in skeletal muscle

E

B3.3.5 Roles of skeletons as anchorage for muscles and as levers

B3.3.6 Movement at a synovial joint

B3.3.7 R ange of motion of a joint

B3.3.8 Internal and external intercostal muscles as example of antagonistic muscle action to facilitate internal body

movements

B3.3.9 Reasons for locomotion

B3.3.10 Adaptations for swimming in marine mammals

293
 Form and function
LHA

B3.3.1 Adaptations for movement as a

universal feature of living organisms

Movement is one of the functions of life. Two types of movement c an be

distinguished:

s
• movements within the body of an organism such as peristalsis in the gut or

s
ventilation of the lungs

e
• locomotion, which is the movement of an organism from one place

toanother.

r
The former happens in all living organisms. Even in a unicellular organism there

y
are movements within the cytoplasm. The latter happens in some organisms
▴ Figure 3 Bar-tailed godwits (Limosa

butnot all.
lapponica) have ight muscles that they

l
use to beat their wings, generating li and

y
An organism that moves from place to place is motile. M any animals move
–1

n
velocities of up to 90 km h

around while feeding within their territory. Some animals move much greater

t
distances when they migrate. For example, bar-tailed godwits (Limosa lapponica)

O
migrate 10,400km from eastern Siberia to New Zealand in 7–8days. They

i
double their body weight with fat reserves before the journey.

s
An organism that remains in a xed position is sessile. Most plants are sessile,

y
with roots growing into the soil. Most animals are motile. There are some sessile
e
animals, particularly in aquatic or marine habitats. For example, a coral consists

p
of a colony of sessile polyps. In hard corals, the polyps construct a rigid skeleton
v

around themselves. This allows them to extend their tentacles into the water

o
when they are lter-feeding, but they c annot to move to a new loc ation.
i
n

C
U

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

▴ Figure 4 Adult barnacles remain attached to a solid surface, so they are sessile. There are

larval stages in the barnacle life cycle which swim, so they are motile. This photo shows adult

goose barnacles (Lepas anatifera). They are lter-feeding using modied legs that are not

required for motility

294
 Organisms

LHA
B3.3.2 Sliding lament model of muscle

contraction

Muscle bres contain many parallel myobrils. E ach myobril consists of a series

of sarcomeres linked end-to-end at Z-discs. There are light bands at either end

s
of a sarcomere and a dark band in the centre. In relaxed muscle, the Z-discs

s
are further apart, the light bands are wider and overall the sarcomere is longer.

Zlines, dark bands and light bands are visible in electron micrographs.

e
r
relaxed sarcomere

y
relaxed

l
muscle

n
light band light band

O
dark band

i
Z-disc
Z-disc

s
contracted

y
muscle
e
◂ Figure 5 Electron micrographs of

p
relaxed and contracted sarcomeres
contracted sarcomere
v

The pattern of light and dark bands in a sarcomere is due to a precise and regular
o
i

arrangement of two types of protein lament — thin actin laments and thick
n

myosin laments. Actin laments are attached to a Z-disc at one end. The myosin

laments occupy the centre of the sarcomere and interlock like ngers with the
U

actin laments at both ends. E ach myosin lament is surrounded by six actin
n

laments and c an form cross-bridges with them.

dark band
The contraction of sarcomeres, and therefore of muscle, is due to
o
d

the sliding of actin and myosin laments. Myosin laments c ause Z-line light band light band Z-line

this. At regular intervals they have “heads” that form cross-bridges

i
r

by binding to sites along actin laments, spaced at the same

myosin
t

regular intervals. The cross-bridges c an exert a force, using energy

o

from ATP. This pushes the actin lament towards the centre of the
actin

sarcomere, making the actin and myosin laments overlap more.

f

u
x

E ach time the myosin heads bind, they swivel, exerting force which light band shortens,

dark band remains

pushes the actin laments a short distance (8–10 nm) towards the indicating actin
l

the same length

O

centre of the sarcomere. The heads then detach, then swivel back slides along myosin
a

and reattach to the next binding site on the actin. This is sometimes

referred to as a ratchet mechanism. Bec ause of the regular spacing

v

of the heads and the binding sites on the actin, many heads along a

myosin lament bind at the same time. And there are many myosin
E

laments, in many sarcomeres, in many myobrils, in many muscle

bres. There are therefore very large numbers of myosin heads in

sarcomere contracts

muscle. So although each myosin head exerts only a small force,

▴ Figure 6 Diagram of a sarcomere in relaxed muscle

collectively they c an exert very powerful forces.

(above) and contracted muscle (below)

295
 Form and function
LHA

myosin filaments have heads hich



form cross-bridges hen they are

2 ATP binds to the myosin heads

attached to binding sites on actin

and causes them to break the

filaments

cross-bridges by detaching

s
from the binding sites

movement

s
ATP

e
ADP + P

 the ADP and phosphate are

r
released and the heads push the

actin filament inards toards

y
 ATP is hydrolysed to ADP
the centre of the sarcomere-

and phosphate, causing

this is called the poer stroke

l
the myosin heads to

n
ADP + P
change their angle. The

ADP + P
heads are said to be

t
“cocked” in their ne

O
i
 the heads attach to binding sites on
position as they are

actin that are further from the centre of

s
storing potential energy

the sarcomere than the previous sites

from ATP

y
▴ Figure 7 The cycle of stages in the ratchet mechanism that c auses an actin lament to slide over myosin lament
e

p
v

Data-based questions: Transverse sections of striated muscle

o
i

The drawings in Figure 8 show small parts of a myobril, 1. Explain the difference between a transverse and
n

as seen in an electron micrograph of a transverse section alongitudinal section of muscle. [2]

of muscle tissue.

2. Deduce what part of the myofibril is represented

U

bythe drawings as small dots. [2]

n

3. Compare the pattern of dots in the three

diagrams. [3]
o
d

4. Explain the differences between the diagrams in

thepattern of dots. [3]

i
r

t
o

◂ Figure 8 Patterns seen in transverse sections of myobrils

a
f

u
x

B3.3.3 Role of the protein titin and

l
O

antagonistic muscles in muscle relaxation

a

Titin is the largest polypeptide so far discovered. In humans, it is a chain of

v

34,350 amino acids, but in mice it is even longer with 35,213 amino acids.

Titin is elastic and acts like a molecular spring, storing potential energy when it
E

is stretched and releasing this energy when it recoils. Titin connects the end of

myosin laments to the Z-disc and has several functions.

• It holds each myosin filament in the correct position in the centre of six

parallel actin filaments.

• It prevents overstretching of the sarcomere.

• It adds to the force of contraction by releasing energy as it recoils.

296
 Organisms

LHA
Energy is needed to stretch titin and therefore to lengthen a muscle. Lengthening

of muscles happens when they relax. Muscles c an only exert force when they

contract, so a muscle c annot supply the energy it needs to lengthen. The energy

has to be provided by another muscle that is known as the antagonist. Despite

the name, an antagonistic pair of muscles work together, with the contraction of

s
each member of the pair providing the energy needed for lengthening the titin

molecules in the other as it relaxes.

s
e
light dark light

band band band

r
P

y
l
y

n
t

O
i
s
r
Z-disc actin myosin titin

y
(thin filaments) (thick filaments)
e

p
▴ Figure 9 Structure of a sarcomere showing titin laments
v

o
i

B3.3.4 Structure and function of motor units

n

in skeletal muscle

Skeletal muscles are composed of striated muscle bres. These contract when
U

stimulated by a motor neuron. The stimulus is passed from the neuron to the
n

muscle bre at a synapse, using the neurotransmitter acetylcholine. These

synapses are c alled neuromuscular junctions.

o
d

There are many more muscle bres than motor neurons in a typic al skeletal

muscle, bec ause each motor neuron has branches that stimulate dierent
i
r

muscle bres. One motor unit consists of a single motor neuron together with
t
o

all the muscle bres that it stimulates via neuromuscular junctions. There are
a

usually hundreds of muscle bres in a motor unit. These muscle bres are not
f

clumped together in a single group but are mingled with muscle bres of other
u

motorunits.
x

When a nerve impulse passes along the main axon of a motor neuron and then
l
O

along all the branches to the multiple muscle bres in the motor unit, all of the ▴ Figure 10 Motor end plates (boutons)
a

at the ends of branches of a motor neuron

muscle bres respond at the same time by contracting. This helps to achieve a

forming synapses with muscle bres

coordinated contraction of the muscle with as few motor neurons as possible.
v
E

297
 Form and function
LHA

B3.3.5 Roles of skeletons as an anchorage

for muscles and as levers

A skeleton is a hard framework that supports and protects an animal’s body.

Exoskeletons are on the outside of the body whereas endoskeletons are

s
internal. Arthropods such as spiders, crustaceans and insects have exoskeletons

s
consisting of tough plates of chitin that cover most of the body surface.

Vertebrates have endoskeletons consisting of bones.

e
Skeletons facilitate movement by providing an anchorage for muscles and

r
acting as levers. Typic ally, a muscle is attached to two parts of the skeleton.

P
One attachment is the insertion, where muscle contraction c auses movement.

y
The other is the origin and is xed, so contraction does not c ause movement.

For example, the insertion of the masseter muscle is on the jawbone (mandible)

l
and the origin is on the cheek bone, which is part of the skull. Contraction

n
of this muscle moves the jawbone, not the xed cheek bone enabling biting

t
andspeech.

O
i
cheek bone

s
(zygomatic

bone — part of

y
the skull)
e

p
v

t
r

o
o
f
f
e
i
n

joint
C

between the

jawbone and
U

the skull
n

t
n
a
t
l
u
s e
c
e r
r
o
f
o
d

masseter

muscle

▴
i

Figure 12 The eort is further from the fulcrum

jawbone
r

than the resultant force so this lever increases the

t

(mandible)
o

size of the force but decreases the distance moved.

a

▴ Figure 11 Contraction of the masseter muscle c auses the jawbone Bec ause the forces are on opposite sides of the

to move upwards, closing the mouth fulcrum, the direction of the force is reversed
f

u
x

By acting as levers, bones c an change the size and direction of a force (Figure12).
l

A lever has a xed point c alled the fulcrum, which is the pivot point. The force
O

applied to the lever is the eort. When the eort is applied, a resultant force

is exerted at a position on the other side of the fulcrum. If the eort is applied
v

further from the fulcrum than the resultant force, the lever increases the size of

the force, but decreases the distance moved. Conversely, if the eort is applied
E

nearer to the fulcrum than the resultant force, a lever decreases the size of the

force, but increases the distance moved.

298
 Organisms

LHA
For a bone acting as a lever, the fulcrum is the joint where the bone meets another

bone. The eort is applied to the bone by one or more muscles, viatendons.

s
s
e
r
P

y
l
y

n
▴ Figure 13 Skeleton of European mole ▴ Figure 14 Skeleton of cheetah (Acinonyx

(Talpa europaea), with short, wide forelimb jubatus) with long narrow limb bones for

O
bones that are used for digging fast running

i
s
r
B3.3.6 Movement at a synovial joint

y
e
Bones meet at joints. Fixed joints, such as the sutures between bones of the skull,

p
do not allow any movement. Most joints allow bones to move in relation to each
v

other — this is c alled articulation. Most articulated joints have a similar structure

o
and are c alled synovial joints.
i
n

Synovial joints have the following components. cartilage

(pale blue)

• Bones provide an anchorage for muscles and ligaments. By

U

their shape, bones guide the types of movement that c an

capsular
n

occur at a joint.
ligament

synovial fluid

• C artilage is tough, smooth tissue that covers bone at the

(dark blue)
o
d

joint. It helps to prevent friction by preventing contact

ligament

between regions of bone that might otherwise rub together.

between pelvis
pelvis
i

It also absorbs shocks that might c ause bones to fracture.

r

and femur
t

• Synovial fluid fills a c avity in the joint between the c artilages

o

on the ends of the bones. It lubric ates the joint, helping to

a

prevent the friction that would occur if the c artilages were dry
f

and touching.
x

• Ligaments are tough cords of tissue containing large quantities

synovial
femur
l

of the protein collagen. They prevent aberrant movements

membrane
O

that would dislocate or damage the joint. The joint capsule is

(brown)

a tough ligamentous covering to the joint. It seals the joint and

▴
v

Figure 15 The hip joint

holds in the synovial fluid and it helps to prevent dislocation.

• Muscles provide the forces that c ause movement at the joint.

E

• Tendons attach muscle to bone. Like ligaments they

are composed of living tissue, with large quantities of

extracellular collagen, which has high tensile strength. Some

tendons are long and cord-like so forces c an be transmitted

over the distance between the muscle and the bone to which

the tendon attaches it.

299
 Form and function
LHA

Poultry wing dissection

The anatomy of a poultry wing such as a chicken or turkey 2. Cut the skin along the entire length of the wing,

wing is homologous to the human arm. In this dissection, pointing the scissors up so as not to cut the tissues

s
focus on the elbow joint of the poultry wing. underneath.

3. Remove the skin from the wing by placing your finger

s
1st digit

2nd digit under the skin and lightly tearing at the connective

e
tissue below it.

radius
4. Use a blunt probe to separate the individual muscles

r
from each other without tearing them.

y
3rd digit 5. Pull on each of the muscles and note the movement
humerus
ulna

that results. Determine pairs of muscles that are

l
antagonistic.

n
6. Follow a muscle to where it connects to the bones.

scapula

Note the appearance of the tendons.

O
7. C arefully remove the muscles and tendons to expose

i
the ligaments which are white in appearance.

s
▴ Figure 16 Bird wing bones

8. Identify the humerus, the radius and the ulna.

r
1. Rinse the wing under running water and thoroughly

y
9. Separate the bones at the joint and note the

dry it with a paper towel bec ause the surface may be

e
appearance of the c artilage.

p
contaminated with Salmonella bacteria.

10. Note the oily texture of the surface of the c artilage.

v

This is due to synovial fluid.

o
i
n

B3.3.7 R ange of motion of a joint

U

The structure of a joint, including the ligamentous joint c apsule and the
n

ligaments, determines the range movements that are possible. The elbow joint

and the knee joint are hinge joints allowing movements in one plane: exion
o
d

(bending) and extension (straightening). The hip joint, between the pelvis and

the femur, is a ball-and-socket joint. It has a greater range of movement than the
i
r

elbow joint: it c an protract and retract, abduct and adduct, and rotate.
t
o

a
f

protraction
u
x

l
O

outward rotation
a

retraction
v

abduction
E

adduction inward rotation

▴ Figure 17 The hip is a ball-and-socket joint that allows movements in all three planes

300
 Organisms

LHA
The range of movements at a joint c an be investigated by measuring joint angles.

The simplest method is to use a goniometer consisting of two rulers connected to

a protractor (Figure 18). Digital goniometers are available as phone apps. There

are also computer programs that analyse images to obtain measurements of

jointangles.

s
s
Making c areful measurements: Using a goniometer

e
Muscle stretching c an increase the range of motion at a

joint. There are a number of dierent types of stretching

r
regime including dynamic stretching and isometric

P
stretching. Here are some possible research questions.

y
• Does the effect of stretching on the range of motion

l
of a joint persist one day later?

n
• Do the different types of stretching regime differ

t
in terms of the increases they allow in the range of

O
motion of a joint?

i
• Do different joints and types of motion see an

s
increased range of motion after stretching?

y
• How does the range of motion at hip joints compare e
between boys andgirls?

p
v

▴ Figure 18

o
A goniometer
i
n

B3.3.8 Internal and external intercostal

U

muscles as an example of antagonistic muscle

action to facilitate internal body movements

o
d

vertebra
The intercostal muscles are the
i

muscles between the ribs. They are

Ribcage up and out with external intercostal
r

made up of external and internal muscles contracted and internal intercostals

t
o

layers and the muscle bres in these relaxed

a

sternum

layers are orientated dierently. This

f

means that alternating contraction of

u

rib
the dierent layers moves the ribc age
x

in opposite directions. Contraction

l

of the external intercostal muscles

O

blue = external
a

expands the ribc age allowing intercostals

inhalation and stretching of the

v

pink = internal

internal intercostal muscles. This

intercostals

stretching stores potential energy

Ribcage down and in with internal intercostal

E

in the titin in the internal intercostal

muscles contracted and external intercostal

muscles. During exhalation, the

muscles relaxed

internal intercostal muscles contract

and stretch the external intercostal ▴ Figure 19 The internal and external intercostal muscles are antagonistic. They form

muscles. continuous layers of striated muscle between the ribs. In this diagram, pairs of ribs are viewed

from the side, with muscle bres shown at intervals

301
 Form and function
LHA

B3.3.9 Reasons for locomotion

Locomotion requires expenditure of energy, so will only occur if there are benets

for the animal. There are multiple reasons for moving from place to place.

Foraging for food

s
Herbivores move to nd the plant foods that they need. Bees y from ower to

s
ower searching for nectar and pollen. Grazing animals move across grassland

to nd the best pastures. Frugivores move to nd abundant sources of ripe fruit.

e
Predators move to c atch and kill their prey.

r
Esc aping from danger

P
Prey move to esc ape from potential predators or from hostile members of their

y
▴ Figure 20 A diademed sifaka

own species. There is therefore strong selective pressure for rapid movement

(Propithecus diadema) eating wild guava

and/or stamina. M any animals have a roosting site that they return to during times

l
fruit in M antadia National Park, eastern

when they are inactive. Jackdaws (Corvus monedula), for example, gather at dusk

n
M adagasc ar

in roosts with many individuals, oen in treetops, and disperse at dawn.

t
Searching for a mate

O
i
Animals in dispersed populations must travel to nd a mate. By leaving its home

s
territory, an individual animal c an nd an unrelated individual to mate with thus

avoiding inbreeding. Young male lions (Panthera leo), for example, leave the

y
pride of their birth and travele to nd another pride. When they nd a new pride,

they will attempt to displace the dominant male so they c an mate with all the

p
adult females.
v

Migration

M any species of bird migrate in both spring

o and autumn. Some migrate between
i

▴ Figure 21 Springbok antelope the northern and southern hemispheres to avoid the food sc arcities of winter.
n

(Antidorcas marsupialis) in southern Afric a

Others migrate closer to the poles for the summer and back towards the equator

c an esc ape from cheetahs and other

for the winter. For example, snow geese (Anser caerulescens) migrate between
U

predators by running at speeds of over

Arctic North Americ a and the Atlantic coast of the US, breeding in the north and

–1
n

80 km h . They sometimes jump repeatedly

overwintering in the south. Some species such as salmon, c arry out a once-in-a-

to a height of up to 2 m — a behaviour

lifetime migration to their breeding grounds, with the young migrating back to

known as “pronking”. This may alert other

o

the region inhabited by the adults.

d

springbok to dangers or confuse predators

chasing them
i
r

t
o

a
f

u
x

l
O

a
v
E

▴ Figure 22 M ale Americ an moon moths

(Actias luna) have huge antennae that c an

detect pheromones given o by unmated

females hundreds of metres away. This

allows them to y in the direction of a female

▴ Figure 23 S almon migrate from the oceans to their spawning grounds in the headwaters

in order to mate with her

of rivers. Young salmon remain in the river for up to three years and then migrate out to sea

302
 Organisms

LHA
B3.3.10 Adaptations for swimming in

marine mammals

E arly mammals were all terrestrial, but about 50 million years ago some evolved

adaptations for life in water. Water is about a thousand times denser than air and

s
much more viscous. Swimming therefore requires dierent adaptations from

s
those needed for locomotion on land or alo in the air.

e
• Streamlining — marine mammals are shaped to minimize • Airways to allow ventilation of the lungs:

resistance to motion by these features:

– blowhole leading from the larynx to the upper

r
surface of the head, through which marine
– shaped to be widest near the front and tapering

y
mammals breathe
towards the rear, which c auses less drag than

other shapes
– no connection between the mouth and lungs to

l
avoid water entering thelungs.
– flippers, flukes and dorsal fin with an elongated

n
teardrop profile in transverse section which

dorsal fin

reduces drag

O
– body surface smooth due to even distribution of

i
blubber and absence of hind limbs and ear flaps

s
– skin without hair, reducing friction.

y
• Adaptations for locomotion:
e
– flippers, which are used for steering, in place of

p
front legs
v

– flukes on the tail, which are lobes to left and right

that increase thrust when the tail is moved up and

o
i

down
n

– dorsal fin to provide stability by flukes

preventing rolling
U

– blubber, which provides buoyancy, allowing a

blowhole
n

dolphin to cease moving and float just below the

flipper

water surface, for example when it is sleeping.

▴ Figure 24 Streamlining of a dolphin viewed from the side

o
d

(upper drawing) and from above (lower drawing) with transverse

sections through the ipper, dorsal n and uke

i
r

t
o

a
f

u
x

l
O

a
v
E

▴ Figure 25 Internal anatomy of dolphins

303
 Form and function
LHA

Data-based questions: Relationship between movement and food sources

Basking sharks (Cetorhinus maximus) lter feed on

1. Using the sc ale given, c alculate the

zooplankton (small oating marine animals) in temperate

straightline distance:

s
coastal seas. M arine biologists recorded the swimming

a. from point A to point B [1]

paths taken by two basking sharks about 8 km o the

s
b. from point C to point D [1]

coast of Plymouth (UK). At the same time, the densities of

−3

zooplankton (in g m ) were recorded within 3 m of the 2. Distinguish between the swimming

e
swimming path of the sharks. behaviour of shark 1 and shark 2. [1]

r
3. Using the data given, suggest

reasons for the difference in the

y
swimmingbehaviour of the two

sharks. [3]

l
y
4. State two factors other than food

n
which may affect the distribution

t
of the basking sharks. [2]

O
i
s
r

y
e
▴ Figure 26 Paths taken by two basking sharks with densities of zooplankton along

p
the paths
v

o
i

Linking questions
n

1. What are the advantages and disadvantages of dispersal of ospring from

U

their parents?
n

a. List examples of intraspecic competition. (C4.1.10)

b. Distinguish between seed dispersal and pollination in plants.

o
d

(D3.1.12)
i
r

c. Outline reasons for locomotion in living things. (B3.3.9)

t
o

2. What are the relative advantages of versatility and specialization in

a

biologic al mechanisms?
f

a. Distinguish between stem cells and dierentiated cells. (B2.3.2)

u
x

b. Explain how specic immunity develops. (C3.2.8)

l

c. Compare and contrast fundamental and realized niche. (D4.2.12)

O

a
v
E

304
 Organisms

TOK

What counts as a good justic ation for

s
s
aclaim?

e
Knowledge claims require justication for others to accept Experimenters need to have an open mind bec ause

them. In biology, knowledge claims are justied by reference even the act of observation has associated problems. For

r
to empirical evidence. In other words, they are justied by example, an observer might consider that a particular eld

y
observations. Repeated observations lead to hypotheses of view is showing too many or too few stomata. They might

that can be tested by experimentation. A hypothesis is a then reject it as an outlier without including it in the sample.

l
form of generalization. What makes a good generalization? In other words, our expectations c an lead us to be biased

n
One requirement of good generalization is the number of of an observation so that we deem it to be unworthy of

times the phenomenon is observed under similar conditions. inclusion in the data set. This c an be remedied by having a

t
The reliability of quantitative data is increased by repeating quantitative standard for rejecting outliers.

O
i
measurements. For example, Table 1 shows that increasing the

Sometimes a generalization is very surprising. It is possible,

number of respondents in a survey reduces the margin of error.

s
but unlikely, that no stomata are observed on either side of a

r
leaf in a number of samples. In this c ase, it is not reasonable

y
S ample size/N M argin of error/ %

to conclude that this is a new species without stomata. It

e
10 31.6
is more likely that there is a aw in the technique used to

p
detect stomata. This is known as the “coherence test”.
20 22.4
v

o
50 14.1
Generalizations that are found to have predictive power c an
i

100 10.0 lead to the establishment of a theory. Sometimes, reason

n

and theory are reasonable supplements to observation

500 4.5

when it comes to justifying knowledge claims. Plants that

1,000 3.2

come from extreme habitats, such as desert plants and

U

water plants, are expected to have unique distributions

n

▴ Table 1 M argin of error is reduced by increased sample size

of stomata. In what ways do they dier from mesophytes

(plants that live in medium water environments)? Knowledge

Gas exchange occurs through the stomata of leaves. Does
o
d

of the theory of evolution by natural selection leads to

the number of stomata vary within members of a population

explanations of the unique adaptations found in dierent

whose microhabitats vary?
i
r

plants for gas exchange.

t

Repeated counts of the number of stomata visible in the eld

o

of view at high power illustrate the variability of biological

a

material and the need to replicate trials from the same plant.
f

Good generalizations apply in a variety of circumstances. In

x

the case of this experiment, it would be important to observe

many dierent individual plants under the same conditions as

l
O

well as making replicate observations from each individual.

a
v
E

▴ Figure 2 M arram grass (Ammophila arenaria) is a

xerophyte (a plant adapted to dry conditions). It has

unique adaptations such as rolled leaves with stomata

▴ Figure 1 Light micrograph of the epidermis (the upper cell layer) isolated within folds of the rolledleaves

of a tulip leaf

305
 Form and function

End of chapter questions

1. European robins (Erithacus rubecula) migrate south in 2. The graph shows the ventilation rate and tidal volume of

s
the autumn (fall) and north in the spring. They orient a well-trained runner during exercise on a treadmill. The

their direction of flight using the loc al magnetic field, tidal volume is the volume of air being moved in and out

s
which they detect through magnetoreceptors in the of the lungs in each breath.

upper beak. The orientation of the birds in a c aptive

e
80 2.8

environment was studied in spring and autumn, which

2.6

1–

r
are the times of year when the birds normally migrate.
70

1–
nim shtaerb /

htaerb
2.4
The response of the birds to green light, red light and

y
total darkness was investigated. In the figure, triangles
60 2.2

on the edge of circles indic ate the mean direction flown

3
md
2.0

l
by individual birds while the arrows indic ate the overall
50

/
n
mean direction of flight. 1.8

etar

emulov
a. Identify the season and light conditions which 40 1.6

noitalitnev

O
resultin the strongest northerly direction own

1.4

ladit
bythe robins. [1] 30

s
1.2

20 1.0

y
e
9 12 15 18

p
–1
treadmill speed / km h
v

e ventilation rate tidal volume

Source: Amonette, W. and

oDupler, T. The effects of respiratory muscle training
i

on VO 2 max, theventilatory threshold and pulmonary function. JEPonline 2002

n

5(2): 29-35

a. Outline the process of ventilation. [3]

U

b. Distinguish between ventilation and respiration

Source: R Wiltschko et al, The Journal of Experimental Biology, 211 (20),
n

3344-3350 2008
as processes. [2]

b. Distinguish between the eect of red light and

c. Distinguish between the role of external and internal
o
d

greenlight on the behaviour of the robins in spring

intercostal muscles in ventilation. [2]

and autumn (fall). [2]

i

d. State the apparatus used to measure the

r

c. Based on the results of these experiments,

t

tidal volume. [1]

o

suggestone possible conclusion that could be

a

e. C alculate the total volume of air inhaled in 1 minute

drawn regarding the eect of red light on the

during the highest velocity of the treadmill in this

f

behaviour of robins. [1]

u

test, giving the units. [2]

x

d. Using the data in the diagram, deduce, with a

f. Compare and contrast the eect of increasing

reason, whether European robins migrate during the
l

treadmill speed on the ventilation rate and tidal

O

daytime or at night. [2]

a

volume in this runner. [2]

e. Scientists anesthetized the beaks of some robins

3. The body mass index (BMI) is defined as the body

v

inorder to deactivate the magnetoreceptors.

mass divided by the square of the body height, and

Predicthow this would aect their orientation

−2

is expressed in units of k gm (resulting from mass in

E

inredlight. [1]

kilograms and height in metres). A long-term study

followed nearly 40,000 apparently healthy young men

for coronary heart disease (CHD) from adolescence

through adulthood. The results show how the BMI at

adolescence and adulthood affect the risk of CHD. The

BMIs are divided into five groups (quintiles), Q1 being

306
 Organisms

the lowest BMI and Q5 the ii Explain the c auses of rises in saturation. [2]

highest. A risk factor of 2

iii C alculate how long each cycle of falling

or less is desirable.

and rising saturation takes. [2]

a. Determine the BMI of

b. Estimate the minimum oxygen saturation that the

a person with height

s
patient experienced during the night, and when it

of 1.85 mand mass

occurred. [2]

of 100 kg. [1]

s
c. Deduce the sleep patterns of the patient during

b. Using the graph,

e
thenight when the trace was taken. [2]

discuss the hypothesis

that a highBMI in 5. In one research project, pigeons (Columba livia) were

r
adolescence is more trained to take off, fly 35metres and land on a perch.

y
dangerous than ahigh During the flight, the activity of two muscles, the

BMI in adulthood. [2] sternobrachialis (SB) and the thoracobrachialis (TB),

l
was monitored using electromyography. The traces

c. State one factor, other

n
are shown below. The spikes show electric al activity

than BMI, that increases therisk

in contracting muscles. Contraction of the SB muscle

of CHD. [1]

t
c auses a downward movement of the wing.

O
i
Source: Tirosh et al NEJM 2011 364, 1315

take off fast flight landing

s
4. Sometimes the ventilation of the lungs stops. This is

c alled apnea. One possible c ause is the blockage of

r
SB

y
the airways by the soft palate during sleep. This is c alled e
obstructive sleep apnea. It has some potentially harmful

p
consequences, including an increased risk of accidents
TB
v

during the daytime due to disrupted sleep and tiredness.

o
The figure shows the percentage oxygen saturation of
i

400 ms
arterial blood during a night of sleep in a patient with
n

severe obstructive sleep apnea.

a. Outline, using an example, what is meant by

antagonistic muscles. [3]

U

b. Using the data, deduce the number of downstrokes

n

of the wing during the whole ight. [1]

c. Compare the activity of the SB muscle during the

o
d

three phases of the ight. [3]

d. Deduce from the data in the electromyograph

i
r

how the TB muscle is used. [1]

t
o

e. Another muscle, the supracoracoideus, is

a

antagonistic to the SB muscle. State the

f

movement produced by a contraction of

u
x

the supracoracoideus. [1]

l

f. Predict the pattern of the electromyograph

O

trace for the supracoracoideus muscle during

the 35-m ight. [2]

v

g. Explain the role of ATP in vertebrate skeletal

a. Hour 8 shows a typic al pattern due to obstructive

muscle contraction. [4]

sleep apnea.
E

i Explain the c auses of falls in oxygen

saturation (%). [2]

307
 B Fo r m and function

s
s
4 Ecosystems

e
r
The structure of an ecosystem is its form. Ecosystems consist

P
of biotic and abiotic components. The biotic community

y
structure refers to the organisms that are present and the

l
web of interactions between them. Organisms interact

n
in feeding relationships, mutualistic relationships and

t
competitive relationships. Abiotic factors also contribute to

O
i
the overall form of an ecosystem. High levels of rainfall oen

s
result in the development of a forest, moderate levels lead

y
to the development of a grassland ecosystem and sparse
e
rainfall leads to the development of a desert.

p
v

The community structure of the taiga is inuenced

o
by temperature and rainfall. Taiga is a forest biome
i

characterized by high levels of precipitation and cold

n

average annual temperatures. In the taiga, the storage of

nutrients in litter is much higher than in tropic al rainforests.

U

The rate of ow of nutrients from the biomass to the litter is

relatively higher than in the tropic al ecosystem.

o
d

i
r

t
o

a
f

u
x

l
O

a
v
E
B4.1 Adaptation to environment

How are the adaptations and habitats of species related?

s
s
The thick coat of a musk ox is correlated with the low

temperatures of its northerly habitats. The water storage

e
tissue in the stem of a c actus is related to infrequent rainfall

in desert habitats. In biology, characteristics such as these

r
that make an individual suited to its habitat are c alled

y
adaptations. How do adaptations come to exist? What are

other examples of adaptations of organisms to extreme

l
environments? What is the reason that we avoid implying

n
a purpose to an adaptation?

t
▸ Figure 1 Musk ox (Ovibos moschatus) during the autumn,

O
i
Dovreell National Park, Norway

s
r
What c auses the similarities between ecosystems within a terrestrial biome?

y
e
The Wallace line marks a division between species

p
present in similar environments despite their
v

geographic al proximity. Islands to the east and west

of the line have similar environments but very dierent

o
i

species of plant and animal. Islands to the west of the

n

line have Asian species and islands to the east have

Australasian species. What is a possible explanation

U

for this phenomenon? Wherever any particular type of

n

environment occurs in the world, despite geographic

separation, the same forms of plant and animal tend

o

to evolve independently. What is the mechanism that

d

leads to this convergence?

i
r

Every terrestrial environment poses challenges and

t

adaptations are needed for plants and animals to

o

survive and thrive. Wherever any particular type of

▴ Figure 2 The Wallace line runs between Borneo and the K-shaped

environment occurs in the world, despite geographic

f

island of Sulawesi
u

separation, the same forms of plant and animal tend to

x

evolve and therefore similar ecosystems. What is the

l

mechanism that leads to this convergence?

O

SL and HL

B4.1.1 Habitat as the place in which a community, species, population or organism lives
v

B4.1.2 Adaptations of organisms to the abiotic environment of their habitat

E

B4.1.3 Abiotic variables aecting species distribution

B4.1.4 R ange of tolerance of a limiting factor

B4.1.5 Conditions required for coral reef formation

B4.1.6 Abiotic factors as the determinants of terrestrial biome distribution

B4.1.7 Biomes as groups of ecosystems with similar communities due to similar abiotic conditions and convergent

evolution

B4.1.8 Adaptations to life in hot deserts and tropic al rainforest

309
 Form and function

B4.1.1 Habitat as the place in which

a community, species, population or

organismlives

s
Habitat means “he lives” or “she lives” in L atin. In biology, it means the place

where an organism lives. This could be the geographic al loc ation — where

s
in the world. More usually, it means the type of place inhabited: the physic al

e
conditions, the type of ecosystem and where within the ecosystem. It c an apply

to one organism or a whole population, species or community.

r
As an example, the habitat of Ranunculus glacialis is at very high altitude in the

y
Alps and other mountains in Europe, on sites that are snow-covered through the

winter and where there is little competition from other plants. These sites have a

l
short growing season with intense sunlight. R. glacialis grows on acidic soils that

n
are moist but also well drained.

O
i
s
r

y
e

p
v

o
i
n

C
U

n
o
d

i
r

t
o

▴ Figure 3 Glacier crowfoot (R. glacialis) growing at over 2,400m altitude on a northeast

facing slope of limestone rock on the M assif des Diablerets in the Alps
f

u
x

B4.1.2 Adaptations of organisms to the

l
O

abiotic environment of their habitat

a

The environment of an organism is everything that is around it. This includes

v

other living organisms and non-living materials such as air, water and rock.

Living things are referred to as biotic factors and non-living things are c alled
E

abiotic factors. Biotic factors dominate in ecosystems where there are dense

communities of organisms — for example, in tropic al rainforests. Abiotic factors

have more inuence in extreme habitats where population densities are low — for

example, desert or taiga. All organisms are adapted to their abiotic environment.

This is clearly seen in plants that live in extreme habitats such as sand dunes and

mangrove swamps.

310
 Ecosystems

Adaptations of grasses to sand dunes

S and dunes are mounds of sand that form from wind-blown sand in deserts

and at the top of beaches. The challenges for plants on beach dunes are water

conservation and tolerance of high salt concentrations and sand accumulation.

S and retains little water aer rainfall and dunes initially contain little organic matter

s
(which helps to store water in soils). Also, sand on beach dunes c an contain

s
high salt concentrations which hinders water uptake by osmosis. For these

reasons, most types of plant would die of dehydration on sand dunes, so special

e
adaptations are required for growth. Grasses are the dominant plant on beach

▴ Figure 4 Lyme grass on the M a-le’l

dunes in many parts of the world. Lyme grass (Leymus mollis) occurs where sand is

r
Dunes, Humboldt Bay, C alifornia

accumulating at the seaward edge of dunes in North Americ a.

y
Lyme grass has these adaptations:

l
• thick waxy cuticle on leaves to reduce transpiration

n
• stomata in indentations (furrows) where humid air c an remain even in windy

t
conditions

O
i
• leaves that c an roll up during droughts, creating a humid chamber and

reducing the surface area exposed to wind

s
• tough sclerenchyma to prevent wilting during droughts

y
• rhizomes (underground stems) that grow upwards as sand accumulates and
e
extend deep into the dune to obtain water

p
• accumulation of c arbohydrates known as fructans in root and leaf cells to
v

increase osmotic potential and thus water uptake.

o
i

Adaptations of trees to mangrove swamps

n

Mangrove swamps develop on the coast in the tropics and subtropics where

there are sheltered conditions and mud accumulates. These swamps are ooded
U

with seawater at high tide. The dominant species are trees. The environmental
n

challenges are waterlogged anaerobic soils and high salt concentrations. The salt

concentration of the mud can be twice as high as that of seawater. This is due to the
o

daily ooding with seawater and evaporation concentrating the salt in themud.
d

▴ Figure 5 Part of a lyme grass leaf

M angrove trees have the following adaptations that allow them to thrive in a
i

showing tough sclerenchyma (pink) and

r

habitat that would be intolerable for most species:

furrows (visible on the le side in this

t
o

• secretion of excess salt from salt glands in the leaf micrograph) with stomata at their base
a

• root epidermis coated in suberin (cork) which reduces

f

permeability to salt and prevents excessive absorption

u
x

• c able roots growing close to the soil surface where there

l

is most oxygen
O

• pneumatophores, which are vertic al root branches

thatgrow up into the air and c an absorb oxygen for usein

v

roots

• stilt roots that grow out in a downward arch from the

E

central trunk to buttress the tree in the soft mud

• large buoyant seeds that c an be c arried by the ocean to

distant muddy shores

• accumulation of mineral ions and c arbon compounds

▴ Figure 6 The mud in mangrove swamps is decient in oxygen.

such as mannitol, which increases the osmotic potential

M angrove trees have evolved vertic al roots c alled pneumatophores

of root and leaf cells, allowing water absorption from the which they use to obtain oxygen from the air

very saline environment.

311
 Form and function

B4.1.3 Abiotic variables aecting species

distribution

The distribution of a species is where it lives in the world, so it c an be shown on

a map. Distribution maps reect the factors that aect species, especially abiotic

s
factors. The adaptations of plants and animals suit them for living in some physic al

s
environments but not others.

e
Plant distributions are aected by temperature, water availability, light intensity,

soil pH, soil salinity, and the availability of mineral nutrients. Every plant species

r
has a range of tolerance for each of these factors. This means that a plant

P
c annot grow in areas that are outside its range for one or more of the factors.

y
For example, plant species from the tropics are not adapted to survive frosts

so they would not survive in northern regions. Plants from these northern

l
regions have chemic als in their cells that act like antifreeze and prevent frost

n
▴ Figure 7 Distribution of Ranunculus
damage c ausedby the formation of ice crystals. However, the northern plant

glacialis in Sc andinavia. The species range

t
species do not have adaptations for growth in the tropics. They would transpire

O
is shown in green and the centre of gravity
excessively, and their method of photosynthesis would be very inecient at

i
of the range in red

hightemperatures.

s
Animal distributions are aected by abiotic factors such as water availability

y
and temperature. Extremes e of temperature require special adaptations. The

large earsof elephants with their dense networks of surface blood help to

p
dissipate heat in hot climates, whereas polar bears have relatively small ears,
v

minimizing heat loss in Arctic habitats. Some animals have adaptations for life

o
in arid conditions. For example, desert rats have longer loops of Henle in their
i

kidneys to minimize water loss. The adaptations required by aquatic animals are
n

verydierent.

In some c ases, animal distribution is limited by requirements for one stage in the
U

life cycle. S almon require fast owing freshwater streams no more than 3 m deep
n

for spawning. They must have gravel substrates with particle size between 10 mm

and 100 mm and a water pH of between 5.5 and 8.0. As with plants, animals
o
d

have a range of tolerance for each abiotic factor, based on their adaptations.
i
r

B4.1.4 R ange of tolerance of a limiting factor

o

Plant and animal species have ranges of tolerance for abiotic variables. For
f

example, many plant species will only grow in soils within a specic pH range;
u
x

some require full sunlight and others only grow in shade. Animal species also

have ranges of tolerance for variables such as salt concentration in aquatic

l

habitats and temperature.

O

R anges of tolerance c an be investigated experimentally, or by nding correlations

v

between the distribution of a species and abiotic variables. For example, a study

in Taiwan of the mosquito, Aedes aegypti found it requires a minimum night-time

E

temperature of13.8°C.

▴ Figure 8 Ecologists surveying on a

Correlations between the distribution of a species and an abiotic variable c an

transect extending from unburned to

burned woodland at Backhouse Tarn, be investigated by mapping the entire species range, by random sampling for

Tasmania example using quadrats, or by sampling along transect lines.

312
 Ecosystems

Transects

Transects c an be used to investigate the tolerance ranges • Belt transects — the abundance of species is estimated

of species to abiotic variables. A transect used for this in the area between two lines separated by a fixed

purpose should span dierent levels of the variables of distance, often 0.5 m or 1.0 m. Abundance c an be

s
interest. For example, a line taken down a slope from assessed using quadrats placed at regular intervals

s
woodland to peat bog might reveal correlations between alongthe belt.

the distribution of plant species and temperature, light

e
• Observational transects — the observer walks along

intensity and soil pH. These and other abiotic variables

a defined route at a defined pace and records

r
c an be measured using electronic sensors and portable

sightings of target species. This method c an be used

data loggers. There are several dierent methods of

to investigate ranges of tolerance and is also used for

y
sampling using a transect.

monitoring changes in population size over time.

• Line intercept sampling — a tape is laid along the

l
ground between two poles and all organisms that

n
touch the line are recorded.

O
i
s
Observations: Making observations with sensors

y
A sensor is a device that records the level of a parameter. • c an take repeated measurements very rapidly

Electronic sensors are now available for many parameters

e
• c an be left to take measurements automatic ally over

p
that are of interest in ecologic al research. A log is a

long periods
v

permanent record of measurements taken at regular

• stored data c an be transferred easily to a computer

o
intervals. D ata logging is digital storage of measurements

for analysis or long-term storage.

i

from electronic sensors. Compact, portable data

loggers have been designed with a sensor to monitor

n

Bec ause of their advantages, data loggers are widely

an environmental condition such as temperature, light

used, both for ecologic al research and other purposes

intensity or pH and an internal memory to record and

U

such as:

store the digital data. These data loggers have many

n

• medic al diagnostics — in all settings from Intensive

advantages:

C are Units to remote areas far from hospitals

• less expensive than many older designs and easy to

o
d

• industries such as food and drink production — for

operate

example, monitoring of fermentation in wineries

• designed to be compact and portable with battery

i
r

• flight recorders on aircraft.

power
t
o

• available for measuring hundreds of different

a

parameters
f

u
x

Data-based questions: Intertidal zonation

O

The kite diagram in Figure 9 illustrates the distribution of of the shaded region indic ates whether the organism
v

common intertidal species 300 m south of Bembridge was abundant, common, frequent, occ asional or rare

Lifeboat Station on the Isle of Wight, UK. The thickness (ACFORis a sc ale of abundance).
E

313
 Form and function

large shallow rock pool

shingle
height above

edge of ledge
sand
chart datum / m

s
Enteromorpha sp.

Fucus spiralis

s
Arenicola marina

Fucus serratus

e
Sargassum muticum

Littorina mariae

r
Anemonia viridis

Littorina littorea

P
Chondrus crispus

y
Patella vulgata

S.balanoides

l
Laminaria digitata

n
Gibbula cineraria

Laurencia pinnatifida

t
Nucella lapillus

O
abundance scale shore distance

i
= 5 m

s
ACFOR

r
▴ Figure 9 Species abundance as a function of distance from spring tide high water mark (the highest

y
point normally reached by salt water)
e

p
1. Examine the kite diagram and explain the methods 5. Several species are only found near the lower
v

used to collect the data. [3] edge of the intertidal zone. Suggest reasons for

o
them being absent from the upper parts of the

2. State the species that is most abundant in the

i

intertidalzone. [3]

survey area. [1]

n

6. Using the data in the kite diagram, predict two

3. Using the sc ale bar, determine the length of the

species that are adapted to the same abiotic

large shallow rock pool. [2]

U

environment. [2]
n

4. Deduce one species adapted to:

7. Suggest one way in which the objectivity of

a. shingle b. sand c. rock pools. [3]

the research could have been improved. [1]

o
d

i
r

pH changes in rock pools

t
o

The pH in natural pools or in articial aquatic mesocosms

f

c an be monitored using data loggers. Ecologists have

u

monitored pH in rock pools on seashores that contain

x

animals and photosynthesizing algae. The pH of the

l

water rises and falls in a 24-hour cycle, due to changes

O

in c arbon dioxide concentration in the water. The lowest

values of about pH 7 are found during the night and

v

the highest values of about pH 10 when there is bright

sunlight during the day. What are the reasons for these
E

maxima andminima?

▴ Figure 10 Rock pool at Limerick Point, Ireland

314
 Ecosystems

Data-based questions: D ata-logging pH in an aquarium

Figure 11 shows the pH and light intensity in an aquarium 1. Explain the changes in light intensity during

containing a varied community of organisms including the experiment. [2]

s
pondweeds, newts and other animals. The data was
2. Determine how many days the data

obtained by data logging using a pH electrode and a light

logging covers. [2]

s
meter. The aquarium was illuminated articially to give a

3. a. Deduce the trend in pH in the light. [1]

24-hour cycle of light and dark using a lamp controlled

e
b. Explain this trend. [2]

bya timer.

r
4. a. Deduce the trend in pH in darkness. [1]

pH sensor (pH)

b. Explain this trend. [2]

y
iht intensity
7.50 100

pH

stinu
90

l
7.45 80

y
yrartira / ytisnetni

n
70

7.40 60

O
50

i
7.35 40

s
30

7.30 20

r
t h i 

y
10
e
7.25 0

p
0/14:02 1/12:07 2/10:12 3/08:17 4/06:23 5/04:28 6/02:33
v

day / hours: minutes

o
i

▴ Figure 11 Changes in pH and light intensity in an aquarium

n

C
U

B4.1.5 Conditions required for coral reef

n

formation
o
d

Coral reefs are biodiverse marine ecosystems. They c an only develop where

conditions are suitable for hard corals, whose skeletons form the rocky structure
i
r

of the reef. Hard corals contain mutualistic zooxanthellae, which need light for
t

photosynthesis. These are the conditions required.

o

• Depth — less than 50m depth of water, so enough light penetrates.

f

• pH — above 7.8 to allow deposition of c alcium c arbonate in the skeleton.

u
x

• S alinity — between 32 and 42 parts per thousand of dissolved ions to avoid

osmotic problems.
l
O

• Clarity — turbidity would prevent penetration of light so the water must beclear.

• Temperature — 23–29°C so both the coral and its zooxanthellae remain healthy.
v
E

315
 Form and function

s
s
e
r
P

y
l
y

n
t

O
i
s
r

y
e
▴ Figure 12 Coral reefs c an develop between 35° north and 35° south of the Equator

p
v

o
i
n

C
U

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

▴ Figure 13 Hard corals build the reef and provide a habitat for many other species. The blue-green sh on this Pacic reef are

Chromis viridis

316
 Ecosystems

B4.1.6 Abiotic factors as the determinants

ofterrestrial biome distribution

With any combination of abiotic factors, one particular type of ecosystem is likely

to develop. The species composition of the ecosystem will vary depending on

s
the geographic al loc ation, but the adaptations of the species are likely to be

s
similar. All ecosystems of a specic type are a biome.

e
Two abiotic factors are the principal determinants of biome distribution on

E arth: temperature and rainfall. The most likely ecosystem given any particular

r
combination of these factors c an be shown using a graph, with mean annual

P
precipitation on one axis and mean annual temperature on the other.

y
l
y

n
400

O
mc / noitatipicerp launna

i
s
tropical

300

rainforest

temperate

y
rainforest
e

p
tropical

200

seasonal
v

temperate

forest

o
seasonal forest
i

savanna
n

/
100 d
n
la
d
taiga o
d
o n
w la
b
u
r
h
s
U

hot

nd
la
ss
tundra gra
te
ra desert
pe
n

m sert
de
te cold

10 0 10 20 30
o
d

average annual temperature / °C

Gymnocalycium baldianum

▴
i

Figure 14 Relationship between temperature, rainfall and biomes

r

t
o

a
f

B4.1.7 Biomes as groups of ecosystems with

u
x

10 mm
similar communities due to similar abiotic
l
O

Euphorbia obesa

conditions and convergent evolution

a

Biomes are groups of ecosystems that resemble each other, even though they
v

swollen stem
may be widely separated in the world. The resemblance is due to the similar

abiotic conditions, with plants and animals evolving similar adaptations in

E

response to the conditions. This is an example of convergent evolution. By

natural selection, distantly related species that face the same problems nd the

5 mm

same solutions. For example, plants in deserts develop adaptations for water

conservation and storage. C acti in Americ a and euphorbias in Afric a have very
▴ Figure 15 Gymnocalycium baldianum

similar adaptations, despite not being closely related. In some c ases, it is only (a c actus) and Euphorbia obesa

when they produce owers that these desert plants c an be distinguished. (a euphorbia), both viewed from above

317
 Form and function

Tropic al Temperate Taiga (boreal Hot desert Grassland Tundra

forest forest forest)

Temperature high medium low high high/medium very low

Precipitation high high/medium high/medium very low medium medium/low

s
Light intensity high medium medium/low high high/medium low

s
Seasonal minimal in warm summers short summers; minimal variation with a very short

e
variation rainforests colder winters long, cold variation dry season or summer; very

winters cold season cold winter

r
▴ Table 1 E ach of the major biomes is characterized by particular climatic conditions

y
l
y

n
t

O
i
afro-alpine

s
r

y
e

p
v

heathland / chapparal

o
i
n

upper montane forest

U

bamboo forest
o
d

lower montane forest

i
r

t
o

farmed land
f

u
x

▴ Figure 16 In this satellite image of Mount Kenya, dierent ecosystems are visible. The summit is snow
l

covered. Descending eastwards, the ecosystems are afro-alpine (light brown), heathland/chaparral
O

(grey-green), upper montane forest (dark green), bamboo forest (light green), lower montane forest (dark
a

green) with farmed land (mixed colours) outside the boundary of the protected area
v
E

318
 Ecosystems

B4.1.8 Adaptations to life in hot deserts and

tropic al rainforest

Hot deserts are characterized by very high daytime temperatures and much

colder nights. R ainfall totals per year are very low and there c an be long periods

s
without any precipitation. Soil development is very limited, with little organic

s
matter of soil organisms. The saguaro and fennec fox are examples of organisms

adapted to these conditions.

e
The saguaro is a species of c actus that is adapted to life in hot deserts. It has the

r
following adaptations:

y
• a wide-spreading root system to collect water up to 30m from the stem

• deep tap roots that collect water from up to 1 m down in the subsoil

l
y
• fat stems with storage tissue to conserve water after infrequent desert rains

n
• pleated stems that allow shrinkage in droughts and swelling after rains

O
• vertic al orientation of stems to reduce interception of sunlight at midday and

i
▴ Figure 17 S aguaro (Carnegiea

maximize it at cooler times ofday

gigantea) in hot desert in Arizona

s
• a thick waxy cuticle on the stem epidermis to reduce transpiration

y
• leaves reduced to spines, to reduce the surface area for transpiration and

prevent herbivores from eating the slow-growing c actus

e

p
• CAM metabolism allowing stomata to open at night and close during the
v

heat of the day, reducing transpiration.

o
i

The fennec fox is a species of mammal that it adapted to life in hot deserts. It has
n

the following adaptations:

• nocturnal so it avoids the highest temperatures during daylight hours

U

• it builds an underground den where it c an stay cool during the day

n

▴ Figure 18 Fennec fox (Vulpes zerda) at

• long thick hair to provide heat insulation both for the cold nights and

Farafra oasis, Egypt

hot days
o
d

• hairs covering the pads of the feet to provide insulation when walking on

very hot sand

i
r

• a pale-coloured coat that reflects sunlight (a darker coat would absorb it)
t
o

• large ears that radiate heat and help keep body temperature down
a

• a variable ventilation rate that c an be increased to more than 600 breaths per
f

minute (panting) to c ause heat loss by evaporation.

x

Tropic al rainforests are characterized by high temperatures, high precipitation

l
O

and high light intensity. The yellow meranti and the spider monkey are examples
a

of organisms adapted to these conditions.

v

The meranti (Shorea faguetiana) is a species of tree that is adapted to life in

tropic al rainforests. It has the following adaptations:

E

• it c an grow to over 100m high, overtopping other trees and avoiding

competition for light

• trunk of hard dense wood to provide support especially against the

wind stress ▴ Figure 19 Yellow meranti (Shorea

faguetiana) near the Kinabatangan River in

Borneo

319
 Form and function

• trunk is buttressed at the base to provide increased support bec ause

rainforest soils are shallow

• smooth trunk to shed rainwater rapidly

• broad oval leaves with pointed tips that shed rainwater rapidly

s
• evergreen leaves which take advantage of ideal conditions for

photosynthesis throughout the year

s
• enzymes of photosynthesis adapted to tolerate temperatures as high as 35°C

e
• flowers and seed produced in large quantities about one year in five, with

r
none in other years to deter species that eat the seeds.

y
The spider monkey (Atelesgeoroyi) is a species of mammal that is adapted to life

in rainforests. It has the following adaptations:

l
• long arms and legs for climbing and reaching for fruit

n
• flexible shoulders allowing swinging from tree to tree

t
• large hook-like hands without thumbs that c an grasp branches and lianas and

O
i
pick fruit

s
• feet that c an act like extra hands, grasping branches and allowing the arms to

be used for feeding or other purposes

y
• long tail that c an grip onto branches and act like a fifthhand
e

p
• highly developed larynx allowing a wide range of sounds to be made to

communic ate in the dense rainforest c anopy

v

o
• sleeping at night and active in the daytime when vision is most acute and
i

distances c an be judged between branches.

n

▴ Figure 20 Spider monkey (Ateles

• breeding at any time of year as there is a constant supply of fruit, nuts, seeds,

georoyi) in Belize buds, flowers, insects andeggs.

U

Linking questions
o
d

1. What are the properties of the components of biologic al systems?

i
r

a. Explain the interactions between auxin and cytokinin as a means of

t

regulating root and shoot growth. (C3.1.22)

o

b. Discuss the statement: “integration results in emergent properties”.

(C3.1.2)
f

c. Outline the role of feedback control in the regulation of the human

x

heart rate. (C3.1.14)

l
O

2. Is light essential for life?

a

a. Explain why the energy content of each trophic level decreases

v

through a food chain. (C4.2.14)

b. Explain how photosynthesis results in an increase in biomass.

E

(C4.2.15)

c. Outline how chemosynthesis represents an exception to the rule that

ecosystems are dependent on light as a source of energy. (B4.2.6)

320
B4.2 Ecologic al niches

What are the advantages of specialized modes of nutrition to living organisms?

s
s
When Charles D arwin was sent a M adagasc ar star orchid

(Angraecum sesquipedale), which has a 300 mm long nectar tube, he

e
predicted that a moth with equally long tubular mouthparts must exist in

the same ecosystem to act as the orchid’s pollinator. The moth was nally

r
discovered 21years aer D arwin’s death and named Xanthopan praedicta.

y
Its mouthparts are indeed 300 mm long and have to be coiled up when not

in use. They unroll like a party blower when the moth is about to insert them

l
into the nectar tube. On what do you think D arwin based his prediction?

n
t

O
i
s
▴ Figure 1 Xanthopan praedicta

y
e

p
How are the adaptations of a species related to its niche in an ecosystem?
v

o
Kettlehole ponds ll landsc ape features created by retreating glaciers.
i

Circular zones of dierent plants c an be seen at dierent depths in the

n

pond. The deeper the water, the less light penetrates and the lower the

oxygen concentration in mud at the base of the pond. Drying in summer

is the main challenge in shallow water near the margins of the pond,
U

so dierent structural adaptations are benecial, thus dierent species

n

dominate at the edges. Which types of plants would thrive in the centre of

the pond? Which would thrive at theedges?

o
d

i
r

▴ Figure 2 Kettlehole pond

t
o

SL and HL
f

B4.2.1 Ecologic al niche as the role of a species in an ecosystem

x

B4.2.2 Dierences between organisms that are obligate anaerobes, facultative anaerobes and obligate aerobes

B4.2.3 Photosynthesis as the mode of nutrition in plants, algae and several groups of photosynthetic prokaryotes
l
O

B4.2.4 Holozoic nutrition in animals

a

B4.2.5 Mixotrophic nutrition in some protists

B4.2.6 S aprotrophic nutrition in some fungi and bacteria

v

B4.2.7 Diversity of nutrition in archaea

B4.2.8 Relationship between dentition and the diet of omnivorous and herbivorous representative members of the family
E

Hominidae

B4.2.9 Adaptations of herbivores for feeding on plants and of plants for resisting herbivory

B4.2.10 Adaptations of predators for nding, c atching and killing prey and of prey animals for resisting predation

B4.2.11 Adaptations of plant form for harvesting light

B4.2.12 Fundamental and realized niches

B4.2.13 Competitive exclusion and the uniqueness of ecologic al niches

321
 Form and function

B4.2.1 Ecologic al niche as the role

of a species in an ecosystem

One of the central hypotheses of ecology is that every species in an ecosystem

fulls a unique role, c alled its ecologic al niche. Ecologic al niches have both biotic

s
and abiotic elements.

s
• Zones of tolerance for abiotic variables determine the habitat of a

e
species — where it lives in the ecosystem.

• Food is obtained either by synthesis using light, water and c arbon dioxide or

r
by taking it in from other organisms. To minimize competition, species must

P
specialize. To compete effectively, they must develop adaptations for the

y
mode of nutrition that is their specialism.

l
• Other species are utilized to provide a diverse range of services — for example,

n
the supply of mineral elements by recycling, pollination of flowers or dispersal

of seeds; the support provided by the trunks and branches of trees.

O
The ecologic al niche of a species is made up of very many factors — it is

i
multidimensional. Unless all the dimensions of the niche are satised in an

s
ecosystem, a species will not be able to survive, grow or reproduce.

y
e

p
v

o
i
n

C
U

30
 / d n u o rg

20 2
4
o
d
e v ob a

5
r
t hg i e h

10
t

1
o

0.5
a
f

0
u

2 4 6 8 10 12 14
x

prey length / mm
l
O

▴ Figure 3 Two aspects of the niche of the blue-gray

a

gnatc atcher (Polioptila caerulea) are prey size and

foraging height. The graph shows the percentage of the

v

diet according to these two variables in oak woodland,

in C alifornia. There are many other aspects of this bird’s

E

ecologic al niche ▸ Figure 4 P. caerulea eating a gnat

322
 Ecosystems

B4.2.2 Dierences between organisms

Activity: Winogradsky

that are obligate anaerobes, facultative

columns

anaerobes and obligate aerobes

To make a Winogradsky column,

s
Animals and plants require oxygen for aerobic cell respiration, but some other
mud and water from a pond

organisms do not have this requirement. Some microorganisms c an only live in

s
is placed in a large bottle or

the total absence of molecular oxygen (O ) including some species of bacteria,

measuring cylinder, with a range
2

e
archaea and protozoa. Anoxic (lack of oxygen) conditions occur in swamps,
of other materials. The column

water-logged soil or muds, intestinal tracts (guts) of animals and deep in lakes
is sealed and placed in the light.

r
orseas.
Concentration gradients for

P
oxygen and other substances

y
Living organisms c an be placed in three c ategories according to their oxygen

develop in the column, with

requirements (Table 1).

coloured bands due to groups

l
of bacteria and archaea growing

n
where the concentrations suit

C ategory Requirements Examples

t
them.

O
obligate require a continuous oxygen All animals and plants;

i
aerobes supply so only live in oxic Micrococcus luteus (a skin

s
environments bacterium)

r
obligate inhibited or killed by Clostridium tetani (tetanus

y
anaerobes oxygen so only live in anoxic bacterium), methanogenic
e

p
environments archaea
v

facultative use oxygen if available so live Escherichia coli (a gut

o
anaerobes in oxic or anoxic environments bacterium), Saccharomyces
i

(yeast)
n

▴ Table 1 Oxygen requirements of organisms

U

B4.2.3 Photosynthesis as the mode of

o
d

nutrition in plants, algae and several groups

of photosynthetic prokaryotes
i
r

In photosynthesis, energy from sunlight is used for xing c arbon dioxide and
o

using c arbon from it to produce sugars, amino acids and the many other c arbon
a

compounds on which life is based. There are three groups of photosynthesizers:

f

• plants, including mosses, ferns, conifers and flowering plants

x

• eukaryotic algae including seaweeds that grow on rocky shores and ▴ Figure 5 Winogradsky column in a
l

glass bottle
O

unicellular algae such as Chlorella

a

• several groups of bacteria including cyanobacteria (blue–green bacteria) and

purple bacteria.
v

Photosynthesis therefore occurs in two of the three domains of life: in eukaryotes

E

and bacteria, but not in archaea.

323
 Form and function

B4.2.4 Holozoic nutrition in animals

Animals obtain supplies of c arbohydrates, amino acids and other c arbon

compounds by consuming food. They are heterotrophic, bec ause the c arbon

compounds come from other organisms. Molecules such as polysaccharides

s
and proteins must be digested before they c an be absorbed. Digestion in most

animals happens internally, aer the food has been ingested. This is holozoic

s
nutrition, meaning that whole pieces of food are swallowed before being fully

e
digested.

r
This is the sequence of stages in holozoic nutrition:

1. ingestion — taking the food into the gut

y
2. digestion — breaking large food molecules into smaller molecules

l
3. absorption — transport of digested food across the plasma membrane of

n
epidermis cells and thus into the blood and tissues of the body

t
4. assimilation — using digested foods to synthesize proteins and other

O
macromolecules and thus making them part of the body’s tissues

i
s
5. egestion — voiding undigested material from the end of the gut.

y
Some animals digest their food externally so they are not holozoic. Spiders,

for example, inject digestive enzymes into their prey and suck out the liquids
e

p
produced. They absorb the products of digestion in their gut and then
v

assimilatethem.

o
i

assimilation
n

absorption

digestion
ingestion
egestion
U

n
o

mouth lumen of gut epidermis of gut anus

d

▴ Figure 6 Holozoic nutrition

i
r

t
o

B4.2.5 Mixotrophic nutrition in someprotists

a
f

Autotrophs make their own c arbon compounds from simple substances

u

including c arbon dioxide. Heterotrophs obtain their c arbon compounds from

x

other organisms. Some unicellular eukaryotes (protists) use both methods

l

of nutrition. Organisms that are not exclusively autotrophic or heterotrophic

O

are mixotrophic. F acultative mixotrophs c an be entirely autotrophic, entirely

heterotrophic, or use both modes. Euglena gracilis, for example, has chloroplasts
v

and c arries out photosynthesis when there is sucient light, but it c an also feed

on detritus or smaller organisms by endocytosis, so it is a facultative mixotroph.

E

Obligate mixotrophs c annot grow unless they utilize both autotrophic and

heterotrophic modes of nutrition. This may be bec ause the food that they

consume supplies them with a c arbon compound that they c annot themselves

synthesize. In other c ases, a protist that does not have its own chloroplasts

obtains them by consuming algae. It uses the “klepto-chloroplasts” obtained in

this way for photosynthesis until they degrade and have to be replaced.

324
 Ecosystems

s
s
e
r
P

y
l
y
▴ Figure 7 Arabidopsis thaliana — the autotroph that molecular ▴ Figure 8 Humming birds are heterotrophic; the plants from

n
biologists use as a model plant which they obtain nectar are autotrophic

O
i
s
r

y
e

p
v

o
i
n

▴ Figure 9 Euglena — a facultative mixotroph. Organisms such as ▴ Figure 10 Ochromonas sp. c an make their own food through
U

Euglena do not t into the plant or animal kingdoms so are placed photosynthesis, but c an also uptake both dissolved organic
n

in another kingdom, c alled either Protista nutrients and particulate organic matter, including intact cells
o
d

Data-based questions: Mixotrophy in golden algae

i
r

Two strains of the golden alga Ochromonas were 1.0

o

isolated, from the Atlantic Ocean east of New Jersey

a

(isolate 1393) and from the Pacic Ocean east of Taiwan 0.8
Key
f

mixotrophic growth
(isolate 2951). Their growth rates were measured in
u

1–

0.6 atotrophic growth

x

three combinations of conditions: light but no prey

d / et a r

heterotrophic growth
(autotrophic), prey but no light (heterotrophic) and both
l

0.4
O

prey and light (mixotrophic). The prey supplied to the

a

ht w o rg

algae were Vibriobacteria.

0.2

1. Compare and contrast the growth rates for the

v

twoisolates. [4]

0.0
E

2. Deduce, with reasons, whether isolate 1393 is an

–0.2
obligate mixotroph, a facultative mixotroph,

or not a mixotroph. [3]

1393 2951

3. Discuss the nutrition of isolate 2951. [3] isolate

▴ Figure 11 Growth rates of two isolates of the alga Ochromonas

325
 Form and function

B4.2.6 S aprotrophic nutrition in some fungi

and bacteria

S aprotrophs secrete digestive enzymes into the dead organic matter and digest

it externally. They then absorb the products of digestion. M any types of bacteria

s
and fungi are saprotrophic. They are also known as decomposers bec ause they

s
break down c arbon compounds in dead organic matter and release elements

such as nitrogen into the ecosystem, allowing them to be used again by

e
otherorganisms.

r
P

y
Activity: Determining trophic level

l
By answering a series of simple questions about an organism’s mode of

n
nutrition it is usually possible to deduce what trophic group it is in. The

questions are presented in Figure 13 as a dichotomous key, which consists

t
of a series of pairs of choices. The key works for unicellular and multicellular

O
i
organisms, but not for parasites such as tapeworms or fungi that c ause

s
diseases in plants.

▴ Figure 12 S aprotrophic fungi growing

r
Feeds on dead

y
over the surfaces of dead leaves and
Feeds on living or recently

organic matter =

decomposing them by secreting digestive

killed organisms = CONSUMERS
e
ETRTORES

p
enzymes
v

Eiter ingests organic matter y endocytosis no cell

o alls or y taking it into

i

its gt
n

C
U

START HERE
o
d

i
r

Enzymes not
Cell alls resent No ingestion o organic matter No gt
o

secreted Only
a

reires simle
f

Secretes enzymes into

ions and
u

its environment to digest

comonds sc
x

dead organic matter

as CO =

l

= SAPROTROPHS
AUTOTROPHS
O

▴ Figure 13 A dichotomous key

v
E

326
 Ecosystems

Data-based questions: Fishing down marine food webs

Trophic levels c an be represented by a number indic ating 3. Explain why the mean trophic level might increase

the position of a species within an ecosystem. By with age in an individual fish. [2]

s
denition, the producers occupy the rst trophic level (TL)

4. Deduce the change in age of c aptured fish over

and so have a TL of 1. For primary consumers, TL = 2, and

theperiod shown. [2]

s
so on. The higher the number, the more energy-transfer

5. Explain two advantages of humans c atching and

steps between the organism and the initial xing of the

e
consuming fish at a lower mean trophic level. [4]
Sun’s energy. Trophic levels are not always stated as

r
whole numbers. Fish and other animals that feed at more

Key
3.5 fresh water
than one level oen have estimated mean trophic levels.

P
3.4

y
marine

level cihport naem

One eect of commercial over-shing is the reduction 3.3

3.2

l
in the number of sh that feed at higher trophic levels

y
3.1
(i.e. long-lived sh). The phrase “shing down marine

n
3.0
food webs” refers to the increased tendency for marine

2.9

t
landings to consist of animals that feed at lower trophic

O
2.8

levels (Figure 14).

i
2.7

s
1. Suggest a method that might be used to deduce 2.6

thetrophic level of a fish once it is c aptured. [2] 2.5

y
1970 1975 1980 1985 1990 1995 2000

2. a. Compare the changes in mean trophic level

e
year

of landed fish from marine and freshwater

p
fisheries since 1970. [3] ▴ Figure 14 How the mean trophic level of landed sh has
v

changed over a 30-year period

b. Suggest why there is a dierence in the

twotrends. [2]
o
i
n

C
U

B4.2.7 Diversity of nutrition in archaea

n

There are three domains of life: archaea, bacteria and eukaryotes. The archaea
o

are unicellular and have no nucleus, which is a similarity with bacteria. In other
d

respects archaea are closer to eukaryotes.

i
r

Some types of archaea are adapted to extreme environments such as hot springs,
t

salt lakes and soda lakes. M any are dicult to culture in the laboratory, so they are
o

less well researched than the other domains of life.

f

Archaea are extremely diverse in the energy sources used for ATP production.
u
x

There are three main c ategories:

l

• phototrophic — absorption of light energy by pigments — but pigments other

O

than chlorophyll are used

a

+
2

• chemotrophic — oxidation of inorganic chemic als, for example Fe

v

+
3

ionstoFe

• heterotrophic — oxidation of c arbon compounds obtained from other

E

organisms.

327
 Form and function

B4.2.8 Relationship between dentition

and the diet of omnivorous and herbivorous

representative members of the family

s
Hominidae

s
The family Hominidae includes the genera that contain humans (Homo),

orang-utans (Pongo), gorillas (Gorilla), and chimpanzees (Pan). Some

e
members of the Hominidae have an exclusively herbivorous diet and others

r
are omnivorous — some animal prey is included in the diet. Living members of

the Hominidae show a relationship between diet and dentition. This c an be

y
studied using physic al collections of skulls in natural history museums or digital

collections available online such as those found at eSkeletons.org, a database

l
sponsored by the University of Texas at Austin.

n
The teeth of herbivores tend to be large and at to grind down brous plant

t
tissues. Omnivores tend to have a mix of dierent types of teeth to break down

O
both meat and plants in their diet. Humans have at molars in the back of their

i
mouth to crush and grind food, and sharper c anines and incisors than herbivores

s
to tear tougher food, like meat.

y
Once the structure–function relationships have been established, the diet

▴
e
Figure 15 Chimpanzees have much
of extinct species in the Hominidae c an be inferred from their dentition — for

p
larger c anines than humans
example, in Homo oresiensis and Paranthropus robustus
v

o
i

Activity: Deducing diet

n

Figure 16 shows the fossilized jaw and teeth of an individual of Australopithecus anamensis, who lived about 4.1 million
U

years ago. The jaw in Figure 17 is from a female Homo neanderthalensis who lived more than 110,000 years ago (before

the last glaciation).

n

What, if anything, c an be deduced about their diet?

o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

▴ Figure 16 Jaw of Australopithecus anamensis ▴ Figure 17 Jaw of Homo neanderthalensis

328
 Ecosystems

Theories: Making deductions about diet from fragmentary evidence

A theory in science is a general explanation that is prediction. This may corroborate the theories or show that

widely applic able. Theories c an be based on observed they are false and should be rejected.

s
patterns. Predictions c an be generated from these

Theories about dentition c an also be used to infer the diet

theories by deductive reasoning. If observations are

s
of extinct species of hominid; however, it is not possible

made of dentition in animals with known diets, including

to verify these predictions — we c annot be sure what

herbivores, c arnivores and omnivores, theories c an be

e
the diet of an extinct hominid was. Are such predictions

developed about the structure–function relationships

therefore non-scientic? What if skeletons of prey species

r
of teeth. These theories c an be tested by predicting the

are found in the vicinity of the extinct fossil hominid? C an

diet of living animals from the characteristics of their teeth

P
this increase the certainty?

y
and then checking whether the actual diet matches the

l
y

n
B4.2.9 Adaptations of herbivores for

O
feeding on plants and of plants for resisting

i
s
herbivory

r
Animals that feed exclusively on plants are herbivores. They have structural

y
features that adapt them to their diet. Insect mouthparts show great diversity,
e
but are all homologous — they have been derived by evolution from the same

p
ancestral mouthparts. Most insects are herbivores. Insects that feed on leaves c an
v

be divided into two broad groups:

o
i

• beetles and other insects with jaw-like mouthparts for biting off, chewing and
n

ingesting pieces of leaf

• aphids and other insects with tubular mouthparts for piercing leaves or stems
U

to reach phloem sieve tubes and feed on the sap.

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v

▴ Figure 18 Frog beetle (Sagra buqueti) has chewing ▴ Figure 19 Rose aphids (Macrosiphum rosae) have piercing
E

mouthparts for feeding on leaves mouthparts

329
 Form and function

Plants show a variety of adaptations for deterring herbivore attacks. Some have

tough sharp-pointed spines, so herbivores risk injury when eating it. Others

have stings to c ause pain. M any plants synthesize substances that are toxic to

herbivores. These substances are secondary metabolites. (Primary metabolites

are substances that are part of the basic metabolic pathways of a cell.) They

s
may be stored in any part of a plant, particularly seeds, which are attractive to

herbivores bec ause of their high concentrations of protein and starch or oil.

s
e
r
P

y
l
y

n
t

O
i
s
▴ Figure 20 Spines on a leaf stalk of the

y
fan palm (Saribus rotundifolius)
e

p
v

▴ Figure 21 Stings on the tree nettle (Urtica ferox) which is endemic to New Zealand

o
i

In some c ases, herbivores have responded to toxic compounds in plants by

n

developing metabolic adaptations for detoxifying them. This has resulted in

plant–herbivore specicity, with only a few species of herbivore adapted to feed

U

on a particular plant.
n
o
d

B4.2.10 Adaptations of predators for

nding, c atching and killing prey and of prey

i
r

animals for resisting predation

o

Predators are adapted to nd suitable prey and then c atch and kill it. The prey

may be killed before it is ingested, or it may die inside the predator ’s digestive
f

system. Prey species are adapted to resist predation. Selected examples of

x

▴ Figure 22 Milkweed plants (Asclepias

adaptations are shown in Table 2, but there are many others. These adaptations

tuberosa) synthesize toxic glycosides

l

may be structural, chemic al or behavioural.

O

to deter herbivores, but the milkweed

a

aphid (Aphis nerii) not only tolerates these

glycosides, it also makes itself toxic to

v

predators by accumulating them

E

330
 Ecosystems

Table 2 Some adaptations of prey and predators

Type Predators Prey

Physic al

s
s
e
r
P

y
l
▴ Figure 24 Bu-tip moths (Phalera bucephala)
▴ Figure 23 Vampire bats (Desmodus rotundus) have

n
resemble broken birch twigs, giving them c amouage
unique dentition, with small premolars and no molars, but

when roosting during daylight hours on twigs or on the

relatively large incisors and c anines on their upper jaw

t
ground. This is the time when the night-ying moths are

O
that are pointed and razor-sharp. These are used to pierce

i
most vulnerable to predation
prey, so the vampire c an feed on the blood

s
Chemic al

y
e

p
v

o
i
n

C
U

▴ ▴
n

Figure 25 Black mambas (Dendroaspis polylepis) Figure 26 C aterpillars of the cinnabar moth (Tyria

produce venom containing a mixture of neurotoxins, jacobaeae) feed on ragwort and accumulate toxic

including an inhibitor of the enzyme acetylcholinesterase. alkaloids from it. Their black and yellow stripes are warning
o
d

The venom paralyzes prey when injected via poison fangs. coloration which deters predators. Adults are day-ying,

The snake c an then swallow the prey without it resisting with red and black warning coloration, indicating that they
i
r

retain toxins obtained when the larvae fed on ragwort

t

Behavioural
o

a
f

u
x

l
O

a
v
E

▴ Figure 27 Grizzly bears (Ursus arctos) learn ambush ▴ Figure 28 Blue-striped snappers (Lutjanus kasmira)

strategies for catching migrating salmon either by trial swim in a tight group, oen with sudden changes of

and error or copying others. Some bears wait at the top direction. This “schooling” behaviour reduces the chance

of waterfalls for a sh to jump out of the water. Others put of predation, bec ause threats are more likely to be

their heads underwater and watch for a sh swimming past detected and it is dicult for a predator to c atch any one

individual in the bewildering shoal

331
 Form and function

Behavioural adaptations c an change relatively quickly. For example, in the 1920s

blue tits started feeding on cream from milk bottles delivered to doorsteps.

This behaviour spread rapidly across Europe, but disappeared as rapidly

when deliveries of bottled milk with cream diminished in the 1990s. Structural

adaptations take longer to develop bec ause there must be genetic change, but

s
research on seed-eating nches on the Galápagos Islands shows that their beaks

soon start to change in size and shape when the size of seeds available on an

s
island changes. Chemic al adaptations are usually the slowest to change, bec ause

e
new enzymes may be needed or new ways of regulating enzymes and this may

▴ Figure 29 Blue tit (Cyanistes caeruleus)

take millions of years.

r
feeding on cream aer pecking through the

foil c ap of a milk bottle

y
B4.2.11 Adaptations of plant form for

l
harvesting light

n
In environments where there is enough water for abundant plant growth and

t
temperatures are suitable for photosynthesis, plants compete for light. Forest

O
i
ecosystems develop in such environments. Plants use a variety of strategies in

s
forests for obtaining light, so show great diversity of form.

r
trees in the

y
forest canopy
e
including

p
emergents
v

which are the

o tallest
i

individuals
n

C
U

epiphytes
n
o
d

i
r

t
o

a
f

lianas
x

l
O

a
v

strangler
shade-tolerant
▸ Figure 30 Tropic al rainforest

epiphyte
E

shrubs and
is characterized by great diversity

herbs
of plantform

• Trees have a dominant leading shoot that grows rapidly to great height to

reach the forest c anopy where they are unshaded by other trees.

• Lianas climb through other trees, using them for support. This means lianas

do not need to produce as much xylem tissue (wood) as free-standing trees.

332
 Ecosystems

• Epiphytes grow on the trunks and branches of trees, so they receive higher

light intensity than if they grew on the forest floor, but there is minimal soil for

their roots.

• Strangler epiphytes climb up the trunks of trees encircling them and

outgrowing their branches, to shade out the leaves of the tree. Eventually the

s
tree dies leaving only the epiphyte.

s
• Shade-tolerant shrubs and herbs absorb light reaching the forest floor.

e
r
B4.2.12 Fundamental and realized niches

y
realized

Living organisms tolerate a range of biotic and abiotic conditions, but their fundamental

niche

adaptations do not allow them to survive outside this range. The range of niche

l
tolerance is the fundamental niche of the species. If the species were living

n
without any competitors, it would occupy the entire fundamental niche. In natural

ecosystems, there is competition and typic ally a species is excluded from parts

t
▴ Figure 31 A realized niche is a subset

O
of its fundamental niche by competitors. The actual extent of the potential range
of a fundamental niche. The reductions are

i
that a species occupies is its realized niche.
due to overlaps with the niches of other

s
competitor species

y
B4.2.13 Competitive exclusion and the
e

p
uniqueness of ecologic al niches
v

Where the fundamental niches of two species overlap, one species is expected

to exclude the other from that part of its range by competition. This was
o
i

demonstrated experimentally with the our beetles Tribolium castaneum

n

and Tribolium confusum. When reared together at dierent combinations of

temperature and humidity, T. castaneum usually excluded T. confusum in some

U

combinations but T. confusum was more successful in other combinations. In

n

the pie charts in Table 3, blue segments indic ate the percentage of trials where

T. confusum excluded T. castaneum and orange segments indic ate the converse.
o
d

Table 3 Competition between T. castaneum and T. confusum at various temperatures

and humidity levels

i
r

Humidity
o

Temperature/°C
a

30% 70%
f

u
x

24
l
O

a
v

29
E

34

333
 Form and function

If two species in an ecosystem have overlapping fundamental niches and

one species outcompetes the other in all parts of the fundamental niche, the

outcompeted species does not have a realized niche and will be competitively

excluded from the whole ecosystem. According to ecologic al theory, every

species must have a realized niche that diers from the realized niches of all other

s
species if it is to survive in an ecosystem.

s
e
Data-based questions: Competitive exclusion in

c at-tails

r
P
Typha latifolia and Typha angustifolia are two species of plant that grow on

y
the margins of lakes. The upper graph shows primary production of each

l
species when growing together in a natural ecosystem. The lower graph

y
shows the biomass of transplants of the two species when grown without any

n
competition. Negative depth means growing out of the water.

t
1. Compare and contrast the growth of T. angustifolia and T. latifolia in the

O
i
absence of competition. [4]

s
2. Distinguish between the growth of T. angustifolia with and without

competition from T. latifolia. [2]

y
3. Analyse the data in the graphs using the concepts offundamental and
e

p
realized niches. [4]
v

Key

T. latifolia
o
i

T. angustifolia
n

1,600
U

800
g / s s am
o
d

y rd

‒20
i

20 60 100
e e rf - h s a
r

80
t
o

a
f

40
u
x

l
O

0
a

‒20 20 60 100

water depth / cm
v

▴ Figure 32 Competition in c at-tails

E

334
 Ecosystems

Linking questions

1. What are the relative advantages of specicity and versatility?

a. O utline the role of specicity in enzyme function. (C1.1.7)

s
b. Explain the evidence for evolution provided by the pentadactyl limb.

s
(A4.1.4)

e
c. Explain what is meant by the universality of the genetic code. (A2.1.7)

2. For each form of nutrition, what are the unique inputs, processes and

r
outputs?

y
a. Explain what is meant by holozoic nutrition. (B4.2.4)

l
b. Distinguish between the mechanisms of digestion of detritus feeders

y
and saprotrophs. (C4.2.12)

n
c. O utline one example of mixotrophy. (B4.2.5)

O
i
s
r

y
e

p
v

o
i
n

C
U

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

335
 Form and function

TOK

Are some types of knowledge less open

s
s
to interpretation than others?

e
In everyday language, the word “interpretation” implies

more than one possibility. In biology, there c an be

r
competing explanations for a phenomenon, particularly

y
if there is fragmentary evidence bec ause the subject

material is uncontrollable. In such situations, there is greater

l
tolerance for more than one interpretation. However,

n
knowledge such as the structure of skeletal muscle bres

is not open to interpretation. It is a straightforward matter

t
to verify the consensus view about their structure. This is

O
i
bec ause it is possible to obtain further samples to examine,

and the methods of exploring cellular ultrastructure are ▴ Figure 2 H. oresiensis skull (le) next to computer

s
artwork of a human (H. sapiens) skull (right)
reliable.

y
An example of an area where disagreements due to
e
dierent interpretations persist is in the phylogeny of the red

p
wolf (Canis rufus or C. lupus rufus). The modern population
v

is very small and has hybridized with coyotes. Eorts to

o
bring the population back from extinction have depended
i

on the introduction of animals from other populations.

n

Viewpoints dier as to whether or not the present very

small population of red wolves is worth preserving.

Conservation eorts are expensive and nancial resources

U

for conservation are sc arce. The US Fish and Wildlife

n

Service currently recognizes the red wolf as an endangered

species and grants protected status. The International

o
d

Union for the Conservation of Nature has listed the red wolf

as a critic ally endangered species. However, the red wolf

i
r

is not recognized in the CITES appendices of endangered

▴ Figure 1 The structure of skeletal muscle bres is clearly visible

t

species. One interpretation is that the historic al red wolf is a

o

through microscopy

distinct species whereas the modern red wolves trace some

a

of their ancestry to historic red wolves but hybridization

When a palaeoanthropologist uncovers a skull, it is an
f

with other wolves and coyotes has continued, threatening

artefact of the natural world. Scientists would participate
x

the distinctiveness of the population.

in the analysis of such a bone. However, it is not possible
l

to expand the study by looking at more skulls from the

O

population if only one has been found. This is the c ase

a

of the short-statured Homo oresiensis discovered on

v

the island of Flores in Indonesia. Only one skull from this

species has ever been found, though bones and teeth

E

from 14 other individuals have been uncovered. Tools

and bones of prey species have been found along with

the H. oresiensis skeletal fragments. Some of the skeletal

features suggest a relationship to more primitive species

while others suggest it is a more modern species. One

interpretation is that H. oresiensis is a descendant of H.

erectus that underwent a process known as island dwarsm. ▴ Figure 3 A modern red wolf

336
 Ecosystems

End of chapter questions

1. One method used by microbiologists to distinguish 2. New technologies such as dental topographic analysis

s
between the Archaea and Eubacteria is the are being used to help understand how early Hominids

conditions they need for survival. Both groups include lived. This technique allows the pattern of wear of

s
thermophiles, which are species that are adapted to live teeth over a lifetime to be analysed, revealing what

at high temperatures. The graph shows the optimum types of food were eaten. Teeth from early humans and

e
temperature and minimum pH required for growth Australopithecus afarensis were compared. The upper

r
by selected species of Archaea and thermophilic surfaces of the teeth were analysed for slope. The teeth

Eubacteria. examined were in groups of similar stages of wear to

y
ensure consistency of results. The lower the slope, the
e Archaea thermophiic uacteria

flatter the teeth. Flat teeth are best suited to crushing

C° / erutarepmet

l
110
hard, brittle foods. More shaped teeth are better suited

n
to eating elastic foods such as meat.
100

t
90
Key early Hominids A. afarensis

O
i
seerged / epols
80
40
ht w o rg

s
35
70

r
30

y
60
m u m i tp o

25
e

p
50 20
e c af r u s

0 1 2 3 4 5 6 7 8
15
v

minimum pH supporting growth

o
10
n a em
i

5
Source: DL Valentine (2007), Nature Reviews Microbiology, 5, p316
n

a. State the highest optimum growth temperature

0 1 2 3

recorded for the thermophilic Eubacteria. [1]

wear stages
U

b. State the relationship between minimum pH

n

supporting growth and optimum growth

a. i State what changes occurred to all teeth

temperature for Archaea. [1]

withwear. [1]
o
d

c. Compare the results for the Archaea with those for

ii Compare the teeth of early Hominids with

the thermophilic Eubacteria. [2]

thoseof A.afarensis [2]
i
r

d. With reference to the data, suggest why this

t

b. Using the data, suggest how the diets of early

o

method would not always be suitable for

Hominids and A.afarensis diered. [2]
a

distinguishing between Archaea and thermophilic

c. Suggest what other evidence would help

f

Eubacteria. [2]
u

scientiststo determine what food was eaten by

x

e. State a possible habitat for methanogenic

earlyHominids. [2]

Archaea. [1]
l
O

a
v
E

337
 I n t e ra c t i o n and

s
interdependence

s
e
r
1 Molecules

y
l
Systems are based on interactions, interdependence

n
and integration of components. Systems result in the

t
emergence of new properties at each level of biologic al

O
i
organization. Molecules are particles of matter that c annot

s
be divided into smaller parts without losing their chemical

y
identity. The elements that
e are most useful to organisms

are those whose atoms interact to form molecules, usually

p
by covalent bonding. A covalent bond is an example of
v

interdependence: each of the atoms contributes one of

o
i

the shared electrons in the bond. The properties of the

n

molecules are oen quite dierent from the elements

of which they are composed. Thus the properties of

U

molecules are emergent properties. Molecules c an

n

interact with each other to produce emergent properties.

o

For example the wetness of water or its high heat of

d

vaporization are emergent properties. Consider the skin

i
r

secretions of a hippopotamus. As the hippo spends most

t
o

of the day in the water yet is also very sensitive to both

a

drying out and sunburn, it secretes molecules that serve

f

diverse functions such as skin moisturizer, water repellent

x

and antibiotic. The secretion also serves to regulate the

l

hippo’s temperature on land. Self-defence against disease,

O

thermoregulation and moisture regulation are all emergent

v

properties that result from the properties of molecules and

their interaction with other molecules.

E
C1.1 Enzymes and metabolism

In what ways do enzymes interact with other molecules?

s
s
Enzymes interact with a range of molecules including substrates,

competitive and non-competitive inhibitors, and molecules

e
within cellular structures such as membranes. Cells control

metabolism by regulating enzyme activity. The end products of

r
enzyme-c atalysed reactions oen act as inhibitors. The build-up

P
of substrate c an increase the expression of genes responsible

y
for generating new enzymes, to reduce the concentration of the

l
substrate again. Fireies (family L ampyridae) are a group of species

y
of beetles that are able to produce light as a result of an enzyme-

n
c atalysed reaction in their abdomen. How does the rey regulate

t
the emission of light?

O
▴ Figure 1 A rey

i
s
What are the interdependent components of metabolism?

y
e
Metabolism is the sum of all of the interdependent chemic al reactions

p
within an organism. Some of these chemic al reactions are involved in
v

breaking down molecules to yield usable energy in the form of ATP.

It includes the breakdown of macromolecules into their subunits and

o
i

their re-assembly to make new molecules. The breakdown of toxins

n

and waste products is also part of metabolism. Processes such as

growth, maintenance and repair depend on a complex network of

U

interdependent chemic alreactions.

n

The coloured 3D combined positron emission tomography (PET) and

computed tomography (CT) sc an of a healthy human body (Figure 2)

o
d

shows variations in metabolic activity in the body’s internal organs such

as the brain. Blue shows low activity, green shows intermediate activity ▴ Figure 2
i
r

and red shows high activity. Suggest why part of the leg is green.
t
o

SL and HL AHL only

a

C1.1.1 Enzymes as c atalysts C1.1.11 Intracellular and extracellular enzyme-c atalysed

f

C1.1.2 Role of enzymes in metabolism reactions

x

C1.1.3 Anabolic and c atabolic reactions C1.1.12 Generation of heat energy by the reactions of
l

C1.1.4 Enzymes as globular proteins with an active site for metabolism

O

catalysis C1.1.13 Cyclic al and linear pathways in metabolism

a

C1.1.5 Interactions between substrate and active site to allow C1.1.14 Allosteric sites and non-competitive inhibition
v

induced-t binding C1.1.15 Competitive inhibition as a consequence of an

C1.1.6 Role of molecular motion and substrate–active site inhibitor binding reversibly to an active site
E

collisions in enzyme c atalysis C1.1.16 Regulation of metabolic pathways by feedback

C1.1.7 Relationships between the structure of the active site, inhibition

enzyme–substrate specicity and denaturation C1.1.17 Mechanism-based inhibition as a consequence

C1.1.8 Eects of temperature, pH and substrate concentration of chemic al changes to the active site c aused by the

on the rate of enzymeactivity irreversible binding of aninhibitor

C1.1.9 Measurements in enzyme-c atalysed reactions

C1.1.10 Eect of enzymes on activation energy

339
 Interaction and interdependence

C1.1.1 Enzymes as c atalysts

A c atalyst is a substance that increases the rate of a chemic al reaction but is not

changed by the reaction. Bec ause c atalysts are not used up, they c an c atalyse

reactions many times. This means only small amounts are needed in relation to

s
the quantity of reactants.

s
Platinum is an example of an inorganic c atalyst. It is used in the c atalytic

converters tted to vehicles with combustion engines, to help convert unburned

e
hydroc arbons in exhaust gases to c arbon dioxide and water.

r
Enzymes are biologic al c atalysts. They are made by living cells to speed up

P
biochemic al reactions. In these reactions, enzymes convert substrates into

y
products. A general equation for an enzyme-c atalysed reaction is:

l
y
▴ Figure 3 Cystic brosis c auses the

n
enzyme

pancreatic duct to become blocked with

t
mucus. This prevents digestive enzymes

O
produced by the pancreas from reaching

i
the small intestine. Digestion is therefore

s
much slower than normal. Pills containing

a mixture of enzymes c an help a person

y
with cystic brosis to digest their food. The

photograph shows one day’s supply for a

e

p
person with cystic brosis
If cells did not make enzymes, the chemic al reactions on which life is based
v

would happen very slowly at ambient temperatures. Life processes such as

o
respiration, digestion, growth and movement would all be very slow.
i
n

Data-based questions: The eectiveness of

U

enzymes
n

Dierent enzymes increase rates of reactions by dierent amounts. R atios

comparing the rate of reaction with and without an enzyme allow comparison
o
d

of the eectiveness of dierent enzymes. Table 1 shows the rates of four

reactions with and without an enzyme. The ratio between these rates has
i
r

been c alculated for the rst reaction.

t
o

–1

Reaction rate /s
a

Without With enzyme

f

Enzyme R atio
u

enzyme
x

C arbonic
−1 6 6

1.3 × 10 1.0 × 10 7.7 × 10

l

anhydrase
O

Ketosteroid
–7 4

1.7 × 10 6.4 × 10

isomerase
v

–13 6

Nuclease 1.7 × 10 9.5 × 10

OMP
–16 8

2.8 × 10 3.9 × 10
E

dec arboxylase

▴ Table 1

340
 Molecules

1. Dene the term “rate of reaction”. [2]

2. State which reaction has the slowest rate without an enzyme. [1]

3. State which reaction has the fastest rate with an enzyme. [1]

s
4. C alculate the ratios between the rates of reaction with and without an

enzyme for the second, third and fourth reactions. [2]

s
5. Discuss which of the enzymes is the most eective c atalyst. [2]

e
6. Explain how the enzymes increase the rate of the reactions they

r
c atalyse. [2]

y
l
C1.1.2 Role of enzymes in metabolism

n
Metabolism is the complex network of interdependent and interacting chemic al

reactions that occurs in living organisms. Most of these reactions happen inside

O
cells but there are also some extracellular reactions, for example, digestion of

i
foods in the intestine.

s
There are thousands of metabolic reactions. They form pathways in which one

y
type of molecule is transformed into another by a series of small steps. Most

of these pathways are chains of reactions but there are also some cycles. An
e

p
example of a cycle is shown in Figure 4. M aps showing all the pathways of
v

metabolism are very complex. They are available on the internet, for example in

o
the Kyoto Encyclopedia of Genes and Genomes.
i

CO + NH
n

2 3

enzyme 1
U

carbamoyl phosphate
n

ornithine
o
d

urea

enzyme 2
i
r

enzyme 5
t
o

citrulline arginine
f

u
x

aspartate

fumarate

◂ Figure 4 This cycle of metabolic

l

reactions is used to synthesize urea in liver

O

cells. There are ve reactions, so ve dierent

enzyme 3
enzyme 4
enzymes are required. Can you nd out what
v

argininosuccinate
these enzymes are?

Almost all metabolic reactions are c atalysed by an enzyme. One of the properties
E

of enzymes is their specicity. E ach enzyme c atalyses one specic reaction, or

a specic group of reactions. This is a signic ant dierence between enzymes

and non-biologic al c atalysts such as platinum, which c an c atalyse many dierent

reactions. Bec ause of enzyme specicity, living organisms have to make large

numbers of dierent enzymes. Even a relatively simple prokaryotic cell makes

341
 Interaction and interdependence

hundreds of dierent enzymes. Cells with more complic ated metabolism, such as

liver cells, make thousands of dierent enzymes.

Enzyme specicity has many benets. It allows organisms to control metabolism.

If a cell produces an enzyme, it c an drive a particular reaction that would

s
otherwise happen extremely slowly or not at all. By making more or less of an

enzyme, cells c an control the rate of a reaction. There are also mechanisms for

s
temporarily stopping particular enzymes from working if a reaction is not required

e
for a while. In summary, enzymes give living organisms considerable control over

their metabolism and therefore over their activities and chemic al composition.

r
C1.1.3 Anabolic and c atabolic reactions

y
Metabolism has two parts: anabolism and c atabolism. Anabolic reactions

l
build up smaller molecules into larger ones. These reactions require energy.

n
Photosynthesis is an example of anabolism, bec ause c arbon dioxide, water and

other small molecules are combined to produce larger molecules, using energy

t
from light. In anabolic reactions, macromolecules are produced from monomers,

O
i
using energy from ATP. They are condensation reactions bec ause water is a by-

product. Examples of anabolic reactions include:

s
• protein synthesis (translation) by ribosomes

y
• DNA synthesis (replic ation)
e

p
• synthesis of complex carbohydrates including starch, cellulose and glycogen.
v

C atabolic reactions break down larger molecules into smaller ones, releasing

energy. In some c ases, this energy is c aptured

o by coupling the c atabolic reaction
i

to the synthesis of ATP, which c an then be used in the cell. Examples of c atabolic
n

reactions include:

• digestion of food—in humans this happens in the mouth, stomach and

U

smallintestine
n

▴ Figure 5 An easy way to remember that

• cell respiration—in aerobic respiration, glucose or lipids are oxidized to

anabolic reactions build smaller molecules

c arbon dioxide and water

o
d

into larger ones is to think of the anabolic

steroids that are sometimes misused to

• digestion of complex c arbon compounds—decomposers do this with dead

organic matter.
i

promote “body building”

r

t
o

a
f

u
x

l
O

a
v
E

▴ Figure 6 Anabolic reactions in trees c an lead to a huge accumulation of biomass, as in the Moor Park Oak in Shropshire (le). The tree on

the right was recently blown over in a storm and c atabolic reactions, mainly c arried out by fungi, are now breaking down its macromolecules

342
 Molecules

C1.1.4 Enzymes as globular proteins with an

active site for c atalysis

Enzymes are globular proteins, with precise three-dimensional structure and

chemic al properties that allow them to function as c atalysts. For a re action

s
to be c atalysed, the substrate or substrates must bind to a special region on

s
the surface of the enzyme c alled the active site (see Figure 7). The shape and

chemic al properties of the active site and the substrate match e ach other. This

e
allows the substrate to bind with the enzyme while most other substances

c annot. While the substrate is bound to the active site, it is converted into

r
products. The products are then rele ased, le aving the active site free to

y
c atalyse another re action.

▴ Figure 7 Computer-generated

Active sites vary in size, depending on the size of the substrates. Typic ally,

l
image of the enzyme hexokinase (blue),

just a few amino acids at the active site are essential to create the chemic al

n
with a molecule of its substrate glucose

conditions that change the substrates enough to convert them into products.
(yellow) bound to the active site. A second

t
Oen the amino acids that form the active site are not next to each other in the
substrate, phosphate, binds to the active

O
polypeptides that make up the enzyme. They are brought together by the folding
site and the two substrates are linked to

i
of the polypeptides. For that reason the overall three-dimensionalstructure of the
make glucose phosphate

s
enzyme is crucial. If any part of the enzyme is altered, the structure of the active

r
site may change and c atalysis is unlikely tohappen.

y
e

p
v

C1.1.5 Interactions between substrate and

active site to allow induced-t binding

o
i
n

Interactions between the substrate and the active site of an enzyme are the basis

of c atalysis.
U

• A substrate approaches the active site. Until it is near to the enzyme, the

substrate’s direction of movement is random. When it is close enough to

n

interact, the chemic al properties of the enzyme surface attract the substrate

molecule towards the active site.

o

▴
d

Figure 8 Twelve amino acids form

• The substrate binds to the active site. This used to be compared with a key the active site of sucrase isomaltase. The

fitting into a lock. However, that model is inappropriate bec ause interactions numbers show where each amino acid
i
r

comes in the sequence of the polypeptide.

between the substrate and the active site c ause both to change: bond angles
t
o

For example, LEU-233 shows that the amino

and bond lengths are altered, changing the three-dimensional molecular
a

acid leucine is 233rd in the sequence.

shapes of the substrate and the active site. This is c alled induced-fit binding.

Are any of the 12 amino acids that form

f

• If there is a second substrate, it approaches and binds to another part of the

u

the active site next to each other in the

x

active site. Again, the substrate and the active site c ause changes in each
polypeptide?

other to allow binding (Figure 9).

l
O

1. Active site vac ant 2. First substrate bound 3. Second substrate bound 4. Substrates converted to product
v
E

Product released so active site becomes vac ant

▴ Figure 9

343
 Interaction and interdependence

• Changes to substrate molecules make it easier for bonds within them to

break and new bonds to form, converting substrates into products.

• The products detach from the active site. Without substrates or products

interacting with it, the enzyme’s active site returns to its original state. It is

now empty and available for more substrates to bind, so the c atalytic cycle

s
c an be repeated.

s
e
C1.1.6 Role of molecular motion and substrate–

r
active site collisions in enzyme catalysis

y
A substrate molecule c an only bind with the active site of an enzyme if it moves

very close to it. This happens as a result of molecular motion. When a substrate

l
y
and an active site come together, this is known as a substrate–active site collision.

n
However, it is not like the high velocity impacts that c an happen between

t
vehicles on a road. To understand how substrate–active site collisions occur, we

O
need to think about molecular motion in liquids.

i
s
In a liquid, the molecules are packed closely together but they are free to move.

The direction of each molecule changes repeatedly and at random. If the liquid

y
contains both substrate and enzyme molecules, they will occ asionally come
e
together. The rate at which this happens will increase if there are more (a higher

p
concentration of ) substrate or enzyme molecules or if the temperature increases,
v

leading to faster molecular motion.

o
i

When a collision occurs, the substrate may be at any angle to the active site.

Successful collisions are ones in which the substrate and active site are aligned,
n

so binding c an take place. Some enzymes have chemic al properties that draw

substrates towards the active site or adjust their orientation. However, the forces
U

involved only work over short distances so they only promote binding when a
n

substrate molecule is already very close to the active site.

water

There is some variation in the molecular motion of substrates and enzymes:

o
d

molecules

• M any enzyme-c atalysed reactions happen in the cytoplasm. Substrate

substrates and enzyme are both dissolved in water, so are free to move. In most
i
r

c ases, however, the substrate is a smaller molecule than the enzyme so it

t

part of
o

movesmore.
a

active site enzyme

• Some substrates are very large and do not move much. In these c ases, the
f

▴ Figure 10 Enzyme–substrate collisions.

u

enzyme has to move in relation to the substrate. Enzymes that replic ate or
x

If random movements bring any of the

transcribe DNA do this.

substrate molecules close to the active site

l

• Some enzymes are embedded in membranes and c annot move—they are

with the correct orientation, the substrate
O

immobilized. In these c ases, the substrate has to do all the movement.

c an bind to theactive site
v

C1.1.7 Relationships between the structure

E

of the active site, enzyme–substrate

specicity and denaturation

The shape and chemic al properties of an enzyme’s active site allow substrate

molecules to bind, but not other substances. This is c alled enzyme–substrate

specicity.

344
 Molecules

Some enzymes are absolutely specic and always bind the same substrate. For

example, glucose is the only substrate that binds to the active site of the enzyme

glucokinase. Other enzymes are less specic. For example, hexokinase c an bind

with any one of a group of hexose sugars. Proteases also have broad substrate

specicity, so a few types of protease c an between them digest polypeptides

s
with any amino acid sequence.

s
Enzymes are proteins with a precise three-dimensional shape and an intric ate

e
chemic al structure. This structure depends on relatively weak interactions

between amino acids within the protein, including hydrophobic and hydrogen

r
bonds. These interactions are aected by factors such as heat and acidity, so

enzymes are easily altered. Even if changes happen at a distance from the active

y
site, interactions within the enzyme are likely to aect the active site. Even small

changes to the active site c an prevent binding of substrates, or prevent c atalysis

l
aer binding. As a result, the enzyme will no longer work as a c atalyst. If the

n
changes are too great to be reversed, the enzyme is denatured.

O
i
Data-based questions: Biosynthesis of glycogen

s
In 1947, the Nobel Prize in Physiology or Medicine was 4. Curve A in Figure 12 was obtained using heat-treated

y
won by Gerty Cori and her husband C arl. They isolated enzymes. Explain the shape of curve A. [2]

two enzymes that convert glucose phosphate into

e
5. Curve B in Figure 12 was obtained using enzymes

p
glycogen. Glycogen is a polysaccharide. It is composed of

that had not been heat-treated.

glucose molecules bonded together in two ways, called

v

a. Describe the shape of curve B. [1]

1,4 and 1,6 bonds (see Figure 11).

o
i

b. Explain the shape of curve B. [2]

n

80
B
U

noisrevnoc %
n

60
o
d

40
▴ Figure 11 Bonding in glycogen
i
r

1. Deduce whether the production of glycogen is

20
t

c atabolic or anabolic. Give a reason. [1]

o

A
2. Explain why two dierent enzymes are needed for the
f

synthesis of glycogen from glucose phosphate. [2]

10 20 30 40 50
u

time / min
x

3. The formation of side-branches increases the rate at

▴ Figure 12 Graph showing the percentage conversion of

which glucose phosphate molecules c an be linked
l

glucose phosphate to glycogen by the two groups of enzymes,

O

to a growing glycogen molecule. Explain the

a

over a 50-minute period

reason for this. [2]

v

C1.1.8 Eects of temperature, pH and substrate

E

concentration on the rate of enzyme activity

1. Eects of temperature

Enzyme activity is aected by temperature in two ways.

In liquids, the particles are in continual random motion. When a liquid is heated,

the particles gain kinetic energy. As a result, enzyme and substrate molecules

345
 Interaction and interdependence

rate at which reaction move around more quickly and the chance of a substrate

decreases owing to molecule colliding with the active site of the enzyme is

denaturation of optimum temperature,

increased. Enzyme activity therefore increases.

enzyme molecules which is not always 40 °

and can be much higher When enzymes are heated, bonds in the enzyme vibrate more

s
in the enzymes of organisms
and the chance of these bonds breaking is increased. When

adapted to high ambient

bonds in the enzyme break, the enzyme structure changes.

s
temperatures

Changes to the active site will mean it c an no longer bind with

rate at which

e
substrate molecules: the enzyme is denatured. Dierent enzyme

reaction increases

molecules denature at slightly dierent temperatures. However,

noitcaer fo etar

owing to increased

r
as temperature rises, more and more enzyme molecules
kinetic energy of

in a solution will be denatured and enzyme activity will fall.

substrate and

y
enzyme Eventually, all enzyme molecules will be denatured and c atalysis

molecules
will stop completely.

l
y
As temperature rises, there are reasons for both increases and

n
decreases in enzyme activity. Figure 13 shows the overall eect

t
actual of temperature on a typic alenzyme.

O
rate of

i
2. Eects of pH
reaction

s
Enzymes are sensitive to their chemic al environment. In
0 10 20 30 40 50 60

r
particular they are aected by how acidic or alkaline it is. Acidity

y
temperature  °

is due to the presence of hydrogen ions (protons). The higher

e
▴ Figure 13 Temperature and rate of

p
the hydrogen ion concentration, the more acidic a solution is. The pH sc ale is a

enzymeactivity

measure of hydrogen ion concentration and therefore acidity. Lower pH values

v

indic ate higher hydrogen ion concentrations and therefore greateracidity.

o
i

The pH sc ale is logarithmic. This means that reducing the pH by one unit makes
n

a solution 10 times more acidic. A solution at pH 7 is neutral. A solution at pH 6

is slightly acidic; pH 5 is 10 times more acidic than pH6, pH 4 is 100 times more
U

acidic than pH 6, and so on.

Key
n

stomach Most enzymes have an optimum pH at which their activity is highest. If pH

1

increases or decreases from the optimum, ionic bonds between the amino acids
acidic hot
o
d

springs in the enzyme are altered. This changes the structure of the enzyme, including its
2

active site. As a result, the active site will no longer bind substrates or convert them
decaying plant
i
r

3 to products. Beyond a certain pH, the enzyme will be irreversibly denatured.

matter
t
o

large intestine
4
optimum pH at which enzyme
a

small intestine
activity is fastest (pH 7 is
f

5
alkaline lakes optimum for most enzymes)
u
x

as pH increases or decreases
l

from the optimum, enzyme

O

ytivitca

7
a

activity is reduced. This is because

the shape of the active site is

8
v

emyzne

altered so the substrate does not

fit so well. Most enzymes are

9
E

denatured by very hih or low

10 pH, so the enzyme no loner

catalyses the reaction.

pH
▴ Figure 14 pH variation in

enzymeenvironments
▴ Figure 15 pH and enzyme activity

346
 Molecules

Not all enzymes have the same optimum pH—in fact, there is a wide range.

This reects the varied environments in which enzymes work. For example, the

protease secreted by Bacillus licheniformis has a pH optimum between 9 and

10. This bacterium is cultured to produce its alkaline-tolerant protease for use in

biological laundry detergents, which are alkaline.

s
3. Eects of substrate concentration

s
Enzymes c annot c atalyse a reaction until the substrate binds with the active site.

e
Collisions between substrates and active sites occur due to random movements

of molecules in liquids. If the concentration of substrate molecules is increased,

r
substrate–active site collisions will occur more frequently and the rate at which

ytivitca
the enzyme c atalyses its reaction will increase.

y
However, there is another trend that aects the rate of reaction. Once a substrate

emyzne

l
has bound to an active site, the active site is occupied and unavailable to other

n
substrate molecules until products have been formed and released. As the

substrate concentration rises, more and more of the active sites are occupied at

t
any moment. Therefore, a greater and greater proportion of substrate–active site

O
i
collisions are blocked. For this reason, the increases in the rate at which enzymes

s
c atalyse reactions get smaller and smaller as substrate concentration rises.

substrate concentration

r
If the relationship between substrate concentration and enzyme activity is plotted

y
on a graph, a distinctive curve is seen (Figure 16): the graph rises less and less ▴ Figure 16 The eect of substrate
e

p
steeply as substrate concentration increases, but never quite reaches a maximum. concentration on enzyme activity
v

Data-based questions: Adenylate kinase

o
i
n

The enzyme adenylate kinase consists of a single 1. For the wild type form of the enzyme, identify:

polypeptide of 214amino acids. It c atalyses reversible

a. the optimum temperature [1]

U

reactions in which a phosphate is transferred between

n

b. the temperature above which the enzyme is

nucleotides:

fully denatured. [1]

ATP + AMP → 2ADP
o

The graph in Figure 17 shows the eect of temperature on

d

2. a. State the activity of the wild type form of the

the activity of ve forms of adenylate kinase. WT is the wild enzyme at each of these temperatures: 15°C,
i

type form. The other forms are mutants in which one amino 25°C, 35°C and 45°C. [2]
r

acid (either valine or alanine) has been changed to glycine.

t

b. Using this data, evaluate the hypothesis that

o

enzyme activity doubles with every 10°C

V142G
600 rise in temperature. [2]
f

V135G
u

WT
1–

3. Explain the reasons for the change in activity of the

x
s / ytivitca

450 A55G

wild type form of the enzyme between:

A37G
l
O

a. 15 and 45°C [2]

300
a

b. 50 and 55°C. [2]

150
v

4. Compare and contrast the curves for WT and

V135G. [3]
E

10 20 30 40 50 60
5. Using the data in the graph, describe the eect of

temperature / °C changing the 55th amino acid in adenylate kinase

from alanine to glycine. [2]

▴ Figure 17 Source: S aavedra, H.G., Wrabl, J.O., Anderson, J.A. et al. Dynamic

allostery can drive cold adaptation in enzymes. Nature 558,

324–328 (2018). https://doi.org/10.1038/s41586-018-0183-2

347
 Interaction and interdependence

Models: Use of graphs to show relationships between variables

A graph is used to show the relationship between two independent variable. It may be an individual result, or a

variables. Two axes are needed to do this. The x-axis mean result if repeat measurements were made. Oen the

s
goes across the graph from le to right and the y-axis data points are joined with straight lines, as in Figure17

goes up the graph. An e asy way to remember this is that on the previous page. This indic ates that it is uncertain

s
the x-axis goes across bec ause the letter x is a cross! what the values would have been at other levels of the

e
The independent v ariable in an experiment is plotted on independent variable.

the x-axis and the dependent v ariable is plotted on the

A graph of experimental results c an be used to evaluate

r
y-axis.
the hypothesis—do the actual results match the model

The rst step in any scientic investigation is to formulate shown in the sketch graph? If they do not, then a new

y
a hypothesis. If the hypothesis is an expected relationship hypothesis may be needed. If the data points on the

between two variables, it c an be shown using a graph suggest an overall relationship between the

l
sketch graph. This type of graph is a model—a simple dependent and independent variables, a line may be

n
representation of something more complex. To test the added to show this. This line is c alled a curve, whether

hypothesis, an experiment is performed and the results it is curved or straight. It is usually a “line of best t” that

O
are compared with predictions based on the hypothesis. goes as close as possible to the data points but does not

i
necessarily pass through them all. You should be able to
When the results of an enzyme experiment are plotted

s
look at the shape of a graph and deduce the relationship
on a graph, each data point shows the level of the

between the variables; this will be a useful skill in science.

dependent variable at one particular level of the

y
Some examples are shown below in Figure 18.
e

p
v

y y y

o
i
n

C
U

x x x

0 0 0

There is a positive There is a negative There is no relationship

o
d

correlation between x and y correlation between x and y between between x and y

i
r

y y y
t
o

a
f

u
x

l
O

x x x
a

0 0 0

There is a positive correlation y is inversely As x increases there is

v

between x and y and y is proportional to x an exponential increase in y

directly proportional to x
E

▴ Figure 18

348
 Molecules

C1.1.9 Measurements in enzyme-c atalysed

reactions

Enzyme experiments require accurate measurements, to ensure the results are

reliable. Reliability is demonstrated by repeating an experiment and showing that

s
the results are consistent. There are dierent types of variable in an experiment:

s
• Independent variables—these are factors that are being investigated, so

e
they are deliberately varied to see what the effect is. Often there is just one

independent variable, making data from the experiment easy to analyse.

r
Variables are independent if the researcher has a free choice of what levels

to use. In enzyme experiments, the independent variable is commonly

y
temperature, substrate concentration, enzyme concentration or pH.

• Control variables—these are factors that must be kept constant to ensure the

l
experiment is a “fair test”. Control variables should be monitored regularly

n
to ensure they do not change. In a properly designed enzyme experiment,

t
all factors that could affect enzyme activity—apart from the independent

O
variable—are control variables.

i
• Dependent variables—these are the results of the experiment. In an enzyme

s
experiment, the dependent variable is the quantity that is measured to calculate

y
the reaction rate. Only changes to the independent variable should affect the

level of the dependent variable. This rate is often c alled enzymeactivity.

e

p
C alculation of reaction rates is an important skill, whether you do this using data
v

from your own experiment or secondary data from an experiment c arried out

o
by someone else. Reaction rate is the speed at which substrates are converted
i

to products, so the units are the change in the amount of chemic al divided by
n

−1

time, for example, millimoles per second (mmol s ). There are two approaches to

nding the reaction rate:

U

1. Allow the reaction to happen for a fixed time and measure the amount of
n

substrate used up or product formed. The time should be relatively short, so

the substrate concentration remains high.

o
d

2. Start with a known amount of substrate and allow the reaction to continue

until all the substrate has been converted to products. Measure the time
i

taken for the reaction to go to completion.

r

With both approaches, the quantity of product or substrate is divided by thetime.

o

With enzymes, starch or other macromolecules, concentration is usually

f

measured in grams per cubic decimetre or grams per 100 cm of solution. Grams
u

3 3
x

per 100 cm c an be expressed as a percentage. For example, 100 cm of 1%

starch solution contains 1 gram of starch.

l
O

Q uantity measured Units Method of measurement

mass of enzyme or reagents grams (g) or milligrams (mg) electronic balance

v

3 3

volume of solutions cubic decimetre (dm ) or cubic centimetre (cm ) pipettes or syringes; measuring cylinders
E

−3

molar concentration moles per cubic decimetre (mol dm ) indirect measurement of mass and volume

−3

mass concentration grams per cubic decimetre (g dm ) indirect measurement of mass and volume

temperature Celsius (°C) thermometer; digital temperature probe

acidity pH pH meter; universal indic ator

light absorbance percentage absorbance(%) colorimeter

▴ Table 2 Possible ways of measuring or determining the level of variables in enzyme experiments

349
 Interaction and interdependence

The following example describes one experiment to investigate the rate of an

enzyme-c atalysed reaction. However, there are many other enzymes and ways of

measuring reaction rate.

s
Collecting and processing data: Measuring

s
c atalase activity

e
The apparatus shown in Figure 19 c an be used to investigate the activity

of c atalase. Yeast cells contain c atalase. Yeast mixed with water is injected

r
into the test tube to start the reaction. C atalase c atalyses the conversion of

P
hydrogen peroxide, a toxic by-product of metabolism, into water and oxygen.

y
C atalase is one of the most widespread enzymes and other sources of the

l
enzyme could be used (for example, liver tissue, kidney tissue or germinating

y
seeds). These sources would have to be macerated and then mixed with

n
water before being injected.

O
i
oxygen

s
r

y
measuring cylinder
yeast
e

p
three-way tap

water
v

o
i
n

water

3
0.8 mol dm
U

hydrogen peroxide
n

▴
o

Figure 19 Apparatus for measuring c atalase activity

d

To investigate the eect of substrate concentration, you could measure the

i
r

reaction rate repeatedly using the same concentration of yeast but dierent
t
o

hydrogen peroxide concentrations. Alternatively, you could investigate the

a

eect of varying catalase concentration.

f

1. How c an the activity of c atalase be measured using the apparatus shown

u

in Figure 19? Include suitable SI units for the reaction rate.

x

2. What factors should be kept constant if investigating the eect of substrate

l
O

concentration?
a

−3

3. How c an the 0.8 mol dm hydrogen peroxide solution be diluted to

v

−3

make concentrations of 0.2, 0.4 and 0.6 mol dm ?

4. Why is it necessary to macerate other c atalase sources such as liver tissue

E

before measuring c atalase activity in them?

S afety goggles must be worn if this experiment is performed. C are

should be taken not to get hydrogen peroxide on the skin.

350
 Molecules

Data-based questions: C alculating rates of reaction

3 3

1. 10 cm of 1% starch solution was mixed with 1 cm of 2. Ten drops of a commercial catalase solution were

0.1% amylase solution. The reaction mixture was kept added to four reaction vessels containing a 1.5%

s
at 40°C. A test for starch was done every 30 seconds, hydrogen peroxide solution. Each of the solutions had

using iodine solution. The rst test that showed no been kept at a dierent temperature. The % oxygenin

s
starch was present aer 8 minutes. the reaction vessel was determined using a data

logger in a set-up similar to Figure 20.

e
a. C alculate the mass of starch in the reaction

mixture in grams. [2] a. Explain the variation in oxygen percentage

r
at time zero. [1]

b. Convert this mass to milligrams. [1]

y
b. Use the graph to determine the rate of

c. C alculate the mass of starch digested

reaction at each temperature. [4]

per minute by the amylase. [1]

l
c. Plot a graph of reaction rate against

y
d. Convert this rate of reaction from “per minute”

n
temperature. [3]

to “per second”. [1]

t
d. Discuss whether a logarithmic sc ale for the

O
i
y-axis should be used instead of a linear sc ale. [2]

s
51°C 4°C
22.0

r
21°C 34°C
21.5

y
21.0
e
% / n e g yx o

p
20.5
v

20.0

19.5

o
i

19.0
n

18.5

▴ Figure 20 18.0
U

0 10 20 30 40 50 60 70
n

time / s
o
d

▴ Figure 21 Percentage of oxygen concentration over time at various

temperatures aer adding c atalase to a 1.5% hydrogen peroxide solution

i
r

t
o

ATL Thinking skills: Choosing a method to determine reaction rate

f

u
x

D ata processing involves converting raw data into a form b. Lipase c atalyses the breakdown of triglycerides to

that is easier to interpret. Reaction rate is measured as fatty acids andwater. F atty acids aect the pH of the
l

change in the amount of reactant or product per second. reaction as the reactionproceeds.
O

For each of these enzyme experiments, describe how the

c. Gelatin cubes are digested by papain, which is a

rate of reaction c an be determined:

protease that c an be extracted from papaya fruits.
v

a. Paper discs soaked in the enzyme c atalase are added

d. The enzyme c atechol oxidase c an be extracted from

to dierent concentrations of hydrogen peroxide. The

E

bananas. It converts c atechol to a yellow pigment in

reaction produces oxygen bubbles.

cut fruit. The yellow pigment reacts with oxygen in the

air to turn brown.

351
 Interaction and interdependence

Mathematics: Using logarithmic sc ales

Most graphs have linear scales on the axes. This means that Logs are exponents. Usually 10 is used as the base

the intervals between values on the axes are number for the exponent.

2
equal—for example, the values 0, 1, 2, 3 are spaced

s
100 = 10 , so log 100 = 2

equally. Sometimes a logarithmic scale is more useful. 3

1,000 = 10 , so log 1,000 = 3.

s
Each interval is 10 times larger than the previous one—for

To nd the logarithm for intermediate numbers, use a

example, a scale with 1, 10, 100 and 1,000 equally spaced is

e
c alculator or an online tool.

logarithmic.

2.5465

For example, 352 = 10 , so log 352 is 2.5465.

r
Logarithmic sc ales are useful when a v ariable c an

Example

take a very wide range of v alues and it is dicult to

y
The enzyme experiment described in the data-based
plot the small v alues or se e the dierences betwe en

question on page 351 gave these results for enzyme

them on a graph. They are also useful for testing

l
activity at dierent temperatures: 68 at 15°C, 123 at 25°C,
whether the inc re ase or de c re ase in a v ariable is

n
243 at 35°C and 536 at 45°C. Is there an exponential
truly exponential. With a line ar sc ale, the curve for an

increase in enzyme activity with rising temperatures?

exponential relationship gets ste eper and ste eper; with

t
1. Convert the values for enzyme activity to base 10logs.
a logarithmic sc ale it should be a straight line.

O
i
On a graph, either one or both sc ales c an be logarithmic.
2. Plot the log values on a graph with temperature on the

s
In a log-linear plot, one sc ale is logarithmic and the other
x-axis and the log values for enzyme activity on the

is linear. In a log-log plot, both sc ales are logarithmic.

y-axis. You can use an axis break at the origin.

y
Special graph paper is available for both types of plot.

3. Is it possible to draw a straight line through (or close to)

e
Alternatively, you c an plot graphs with logarithmic sc ales

p
all the points? If so, what conclusions can you draw?

by converting the data to logarithms (logs).

v

o
i

Data-based questions: Interactions between temperature and enzyme activity

n

Changes to the amino acid sequence of enzymes

1
U

can aect how heat-stable they are and how quickly

nim

Sc
n

they convert substrates to products. The graph

lomµ / C°52

10

in Figure22 shows data for the same enzyme

Bc
(isopropylmalate dehydrogenase) from six dierent
o

Bs
d

species of microbe, three of which are adapted to live

in hot conditions. The graph shows the relationship

i
r

ta

between the temperature at which half of the enzyme

Mt
yt i v it c a
t

1
molecules have denatured due to unfolding, and
o

Tt
a

enzyme activity at 25°C. The graph is a log-linear plot.

em y z n e
f

1. What is the advantage of using a logarithmic

u

sc ale for the y-axis on this graph? [2]

x

St

2. a. Which microbe has the most heat-stable

l

0.1
O

form of the enzyme? [1]

a

30 40 50 60 70 80 90 100

b. Which microbe has a form of the enzyme

denaturation midpoint temperature / ° C
v

that c atalyses the reaction most quickly

Saccharomyces cerevisiae (Sc) Methanothermobacter

at 25°C? [1]

Bacillus subtilis (Bs) thermautotrophicus (Mt)

E

3. What trend does the graph show? [2] Thermus thermophilus (Tt)
Bacillus cereus (Bc)

Sulfolobus tokodaii (St)

4. Using the data in the graph, predict the

problems that would beexperienced by:

▴ Figure 22 Source: Akanuma, S., Bessho, M., Kimura, H. et al.

Establishment of mesophilic-like c atalytic properties

a. Bacillus subtilis in a hot spring at 80°C or higher [2]

in a thermophilic enzyme without aecting its

thermal stability. Sci Rep 9, 9346 (2019). https://doi.

b. Sulfolobus tokodaii in the human intestine at 37°C. [2]

org/10.1038/s41598-019-45560-x

352
 Molecules

ATL Communic ation skills: Generating citations

There are many electronic tools to support students in the National Academy of Sciences of the United States of

writing references in a standardized format such as APA America, 44(2), 98–104.

s
or MLA. Google Scholar is one example. Search through
1. To practise referencing, nd the MLA formatted

Google Scholar to nd the public ation you are looking

citation for the article used in the data-based question

s
for. For example, you might search for D aniel Koshland’s
on page 352: Establishment of mesophilic-like

article in the journal PNAS, “Applic ation of a theory of

e
catalytic properties in a thermophilic enzyme without

enzyme specicity to protein synthesis”. Entering this title

aecting its thermal stability

r
into Google Scholar returns a single entry. At the base of

2. What are some of the ways in which APA and MLA

the entry, you will see a menu similar to the following:

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citations dier? Which format is more commonly used

y
Cited by 3078 Related articles All 9 versions in the bibliographies of scientic papers?

l
3. What rules do you need to follow when providing
Clicking on the quotation marks will give you a range of

n
citations in your IBwork? Check with your school
choices. For example, you c an copy the APA citation and

librarian or your IB coordinator.

paste it into a report:

O
Koshland Jr, D. E. (1958). Applic ation of a theory of

i
enzyme specicity to protein synthesis. Proceedings of

s
r

y
C1.1.10 Eect of enzymes on
Questions
e

p
activationenergy
v

1. State the eect on the

Chemic al reactions are not single-step processes. Substrates have to pass

o
activation energy when an

through a transition state before they are converted into products. Energy is
i

enzyme is present.

required to reach this transition state. This is c alled the activation energy and
n

2. Compare the net change

is used to break bonds in substrate molecules. Energy is also released as new

in energy content between

bonds are made and the product is formed.
U

substrates and products for

The le-hand graph in Figure 23 shows these energy changes for a reaction
n

the two systems shown in

c arried out without an enzyme. The reaction is exothermic bec ause there is a net Figure 23.

release of energy. The energy released as new bonds are made is greater than
o
d

3. Suggest why there are two

the activation energy needed to break bonds and reach the transition state.

peaks rather than one in the

i

graph for a reaction c atalysed

r

The right-hand graph in Figure 23 shows energy changes for the same reaction

by an enzyme.
t

when it is catalysed by an enzyme. The net amount of energy released is unchanged

o

but the activation energy is smaller. This is because the bonds in the substrate are
a

4. Explain how lowering the

weakened as it binds to the active site, so less energy is needed to break them. As a
activation energy increases the
f

result, the rate of the reaction increases—typically by a factor of a million or more.

u

rate of the enzyme-controlled

x

reaction.

transition state
l
O

a
v

activation
ygrene

ygrene

transition state

energy
E

activation

energy

substrate
substrate

◂ Figure 23 Graphs showing

product product
activation energy without an

enzyme (le) and with an enzyme

progress of reaction progress of reaction

(right)

353
 Interaction and interdependence
LHA

C1.1.11 Intracellular and extracellular

enzyme-c atalysed reactions

Enzymes are synthesized by ribosomes. Extracellular enzymes (also known as

exoenzymes) are released from the cell and work outside it. They are synthesized

s
by ribosomes attached to the endoplasmic reticulum. Intracellular enzymes, for

s
use inside the cell, are synthesized by free ribosomes in the cytoplasm.

e
Intracellular enzymes c atalyse metabolic pathways such as glycolysis. The

rst reaction in glycolysis is the addition of a phosphate group to the glucose

r
molecule. This reaction is c atalysed by the enzyme hexokinase in the cytoplasm.

P
Some intracellular enzymes work inside organelles—or example, enzymes of the

y
Krebs cycle work in the mitochondrial matrix. One of the Krebs cycle enzymes is

fumarase, which c atalyses the conversion of fumarate to malate.

l
y

n
M any exoenzymes c atalyse the breakdown of larger macromolecules. The

monomers produced c an then pass through the plasma membrane and enter

O
cells. For humans and other multicellular organisms, this process occurs in the

i
digestive system, where solid food is digested by extracellular enzymes.

s
Unicellular heterotrophic archaea, bacteria and fungi cannot take in

r
macromolecules because their cell walls form a barrier so they cannot perform

y
endocytosis. To feed on macromolecules, these microorganisms secrete
e

p
exoenzymes. These enzymes work outside the cell to convert the macromolecules

into monomers, which can then be absorbed across the plasmamembrane.

v

o
i
n

Questions

1. Suggest what the dark blue organelles are in the image.

U

2. Suggest a reason for storing digestive enzymes in

vesicles, instead of secreting them immediately aer

they are produced.

o
d

3. Suggest reasons for the variation in size of the vesicles

i
r

in these cells.
t
o

◂ Figure 24 False-colour sc anning electron micrograph of

a

enzyme-secreting cells in the pancreas, with the cytoplasm

f

coloured pale blue. Before secretion, the enzymes are stored

u

inside membrane-bound sacs c alled vesicles (coloured yellow).

x

The enzymes are secreted into the small intestine via the
l

pancreatic duct and aer activation they help the digestion of

O

c arbohydrates, fats and proteins

v

C1.1.12 Generation of heat energy by the

E

reactions of metabolism

The conversion of energy from one form to another is never 100% ecient. For

example, in metabolic reactions, the products contain less energy than the

reactants. The additional energy is ultimately converted to heat.

354
 Molecules

LHA
Birds and mammals use the heat generated by metabolism to maintain

a body temperature greater than that of their environment. Sometimes

metabolism releases more heat than is needed for this purpose. For

example, during exercise, the human body produces sweat and uses

evaporative cooling to dissipate excess metabolic heat.

s
In very cold conditions, emperor penguins huddle together in groups to

s
take adv antage of the metabolic he at rele ase d by their neighbours. Birds

e
and mammals raise their overall metabolic rate when bas al metabolism

does not rele ase enough he at. They c an do this in several w ays. A

r
human whose core temperature is falling will experience involuntary

muscle contractions known as shivering. This is an adaptation to produce

P
▴ Figure 25 Decomposing manure or

y
he at by contracting the muscles to raise the core temperature. M any

compost c an become very hot, as this

mammals have brown fat tissue. Cells in this tissue have large numbers of

steaming heap shows. What organisms

l
mitochondria that c arry out uncouple d respiration. This allows them to

are responsible for this metabolic heat

n
generate he at by oxidizing substrates without producing ATP.
generation?

O
i
Questions

s
r
1. The electron micrograph in Figure 26 has been given

y
false colour, to make the dierent structures easier
e
to see. What would the natural colour of this cell

p
havebeen?
v

o
2. Explain why stored fat forms large droplets in the
i

cytoplasm.
n

3. Suggest why infants having relatively more brown

adipose tissue than adults.

U

4. Suggest when brown adipocytes will be active in

n

animals that hibernate.

◂ Figure 26 Electron micrograph of part of a heat-generating

o
d

brown adipose cell with many mitochondria (dark green) in the

cytoplasm (pale green) and droplets of fat (pale yellow). The cell’s
i
r

nucleus (purple) is partly visible (lower right)

t
o

a
f

initial

C1.1.13 Cyclic al and linear pathways

u

TREAD substrate
x

BREAD
in metabolism
l

BREED
O

intermediates
Cells c an perform a huge range of chemic al reactions and have thousands of
BLEED
a

dierent types of enzyme to do this. Most enzyme-c atalysed reactions c ause

BLEND

a small change in a substrate. L arge chemic al transformations happen not in

BLIND
v

one large jump but in a sequence of small steps. Together, these steps form a BLINK

end product

metabolic pathway. The word game in Figure 27 is an analogy.

E

▴ Figure 27

Most metabolic pathways involve a chain of reactions. For example, glycolysis

is used by cells to convert glucose into pyruvate (see Figure 28). The metabolic

pathway for glycolysis involves nine dierent chemic al reactions, c atalysed by

nine dierent enzymes. Glycolysis means “glucose-splitting” and is part of cell

respiration. In all but one of the reactions, one molecule of substrate is converted

to one molecule of product. In the other reaction, a six-c arbon sugar is split

355
 Interaction and interdependence
LHA

s
s
e
▴ Figure 28 Glycolysis

r
into two dierent three-c arbon sugars. One of these is converted into a second

molecule of the other sugar (glyceraldehyde-3-phosphate), which is the substrate

y
for the next reaction in the chain. This means the latter stages of the chain happen

twice per glucose molecule.

l
y

n
Branching of metabolic pathways is very common and metabolism as a whole is

a network of interlinked and interdependent pathways. More unusual are cycles

t
of reactions. In a cycle, every intermediate is a product of one reaction and a

O
▾ Figure 29 Simplied versions of the

i
substrate of another reaction. Two examples of cycles, which will be described

C alvin cycle and the Krebs cycle. These

more fully in the next two chapters, are the C alvin cycle and the Krebs cycle.

s
cycles are described in detail in Sections

C1.3.17 and C1.2.12

y
acetyl group C
2

input: 3 CO +
 + 
e
2

p
+

v


3 RuBP

o
2

3 glycerate phosphate

res
i


6 TP
cycle
n

3 P
C alvin

C compound
6 P C compound

6
cycle
3 TP +
 + 
6 P
U

+

+

+
n

+  + 
6 P CO
2
5 TP

6 TP
C
5

compound
o
d

CO
2
i
r

output: 1 TP glucose and

t

other compounds
o

a
f

C1.1.14 Allosteric sites and non-

x

competitiveinhibition
l
O

Every enzyme has an active site, to which the substrate binds. M any enzymes
a

have a second active site where a dierent specic substance c an bind and

unbind. Binding and unbinding c ause the enzyme to change shape, so the
v

second binding site is c alled an allosteric site.

E

Allosteric sites on enzymes have evolved bec ause they allow the activity of an

enzyme to be regulated. Switching between the two alternative states alters the

structure and properties of the enzyme’s active site. In some c ases, binding to

the allosteric site activates an enzyme so it will c atalyse a reaction. In other c ases,

binding prevents c atalysis and the enzyme is reversibly inhibited. Substances that

inhibit an enzyme by binding to the allosteric site rather than the active site do not

compete with substrates, so they are known as non-competitive inhibitors.

356
 Molecules

LHA
substrate competitive

inhibitor

non-

s
competitive

s
inhibitor

no inhibitor so a non-competitive while a competitive

e
the substrate can inhibitor changes the inhibitor remains bound

bind to the active active site so substrates to the active site,

r
site of the enzyme cannot bind substrates cannot bind

y
▴ Figure 30

l
y

n
C1.1.15 Competitive inhibition as a

t
consequence of an inhibitor binding

O
i
reversibly to an active site

s
Competitive enzyme inhibitors bind to the active site of an enzyme. As long

r
as the inhibitor remains bound, the substrate c annot bind and the enzyme

y
c annot c atalyse its re action. Competitive inhibitors are structurally similar to
e
the substrate so they c an bind to the s ame active site. However, unlike the

p
substrate, they are not converte d into products and so remain bound for
v

longer than the substrate.

o
i

When the active site of an enzyme is vac ant, either a substrate or an inhibitor
n

molecule could bind. Whichever molecule arrives rst and binds successfully with

the active site will be the “winner ” in this competition. The extent of inhibition
U

becomes greater if the concentration of the competitive inhibitor increases.

n

If the inhibitor concentration is relatively low and the substrate concentration

is increased, the extent of inhibition will reduce until the enzyme is eectively
o
d

uninhibited. With many more substrate molecules than inhibitor molecules,

substrates almost always arrive at the active site rst. This is not the c ase with
i
r

non-competitive inhibitors, bec ause increases in substrate concentration c annot

t

prevent a non-competitive inhibitor from binding to the allosteric site. This c an be

o

shown on a graph.
a
f

u
x

maximum rate

no inhibitor

of reaction
noitcaer fo etar

l
O

competitive inhibitor
v

non-competitive inhibitor
E

substrate concentration

▴ Figure 31 Eect of substrate concentration on the rate of an enzyme-c atalysed reaction

with no inhibitor (orange) and with a xed low concentration of a competitive inhibitor (red)

or non-competitive inhibitor(blue)

357
 Interaction and interdependence
LHA

Statins—an example of a competitive inhibitor

Statins are medicines that work by competitive enzyme

inhibition. They are used to treat high blood cholesterol, HO

HO

COOH COOH

s
which c an contribute to heart disease. Statins bind to
O
OH

the active site of the enzyme HMG-CoA reductase. The

H
O

s
SCoA

full name of this enzyme is 3-hydroxy-3-methyl-glutaryl-

O

coenzyme A reductase. It c atalyses one of the reactions

e
HMG-CoA

in the metabolic pathway used to synthesize cholesterol

r
in liver cells. This reaction is the rate-limiting step in the

lovastatin

pathway, so if statins lower the rate, less cholesterol

P
▴ Figure 32 Structural similarities between HMG-CoA (the

y
is produced by the body. A person with high-blood

substrate of HMG-CoA reductase) and statins (such as lovastatin

cholesterol must receive the correct dose of statins, so

shown here) allow statins to bind to the active site and act as a

l
cholesterol levels are reduced enough but not too much.

competitiveinhibitor

n
t

O
i
ATL Thinking skills: Evaluating and defending ethic al positions

s
Chemic al weapons would not exist without the activities production of ammonia fertilizer. Such fertilizers have

y
of scientists. For example, sarin is a competitive inhibitor been essential
e in increasing agricultural yields. However,

of the enzyme acetylcholinesterase and has a critic al role some scientists boycotted the award ceremony bec ause

p
in the functioning of the nervous system. It was discovered Haber had been instrumental in encouraging and
v

by German chemist Gerhard Schrader and developed as developing the use of chlorine gas as a chemic al weapon

o
an insecticide. L ater however, it was used as a chemic al during the First World War. Haber is quoted as saying:
i

weapon. Despite being banned by several treaties, sarin “During peacetime a scientist belongs to the World, but
n

has been used in the 21st century. Does Schrader deserve during war time he belongs to his country”. Should Haber

to be described as “the father of nerve agents”? have been recognized for important contributions to

science?
U

Fritz Haber received the 1918 Nobel Prize in Chemistry for

his work in developing the chemistry behind the industrial

n
o
d

C1.1.16 Regulation of metabolic pathways by

i
r

feedback inhibition
t
o

The complex network of metabolic pathways in a cell must be regulated to

a

ensure they produce enough of each substance, but not too much. M any
f

pathways are controlled by a feedback inhibition system. In these systems, the

u
x

product of the last reaction in the pathway—c alled the end product—inhibits the

rst reaction.
l
O

The enzyme that is inhibited has an allosteric site to which the end product binds.

This binding changes the shape of the active site, preventing c atalysis for as
v

long as the end product remains bound. This is an example of non-competitive

inhibition and also negative feedback. If too much of the end product is made, it
E

will increasingly inhibit the rst enzyme in the pathway. This eectively switches

o the whole pathway and prevents synthesis of more end product. If there is too

little of the end product, there will be minimal inhibition of the rst enzyme. The

metabolic pathway will be open to produce more of the end product.

This is a very ecient method of regulating a metabolic pathway. Bec ause the

rst enzyme is inhibited, the products of the intermediate steps in the pathway—

358
 Molecules

LHA
which are only used as steps in making the end product—do
initial substrate

substrate does not fit the

not accumulate in a cell if the end product is not being used.
(threonine)

active site when the end

The metabolic pathway in cells that converts the amino acid

threonine
product is bond
threonine into isoleucine is an example of feedback inhibition

in active site
by an end product.

s
enzyme 1

Through a series of ve reactions, the amino acid threonine

enzyme

s
(threonine

is converted to isoleucine. As the concentration of isoleucine

activated if

deaminase)

e
builds up, it binds to the allosteric site of the rst enzyme in
inhibitor

the chain, threonine deaminase. As a result, it acts as a non-

unbinds
intermediate A

r
competitive inhibitor.

enzyme 2

y
intermediate B

enzyme 3
C1.1.17 Mechanism-based

l
end product

n
intermediate C
inhibition as a consequence of
inhibits the first

enzyme 

enzyme in the

t
chemic al changes to the active site

O
pathway by
intermediate 

i
c aused by the irreversible binding binding to its

enzyme 

s
allosteric site

ofaninhibitor

y
end product

The examples of enzyme inhibition described so far have all

(isoleucine)
e
been reversible. However, inhibition c an also be irreversible.

p
▴ Figure 33
Heavy metals such as mercury and lead are non-specic
v

inhibitors of a wide range of enzymes bec ause they bind

o
irreversibly to –SH groups in the amino acid cysteine wherever it occurs in the
i

structure of an enzyme. For this reason, these heavy metals are very toxic if they
n

enter the body and they are dangerous pollutants of the environment.

Some irreversible inhibitors target one specic enzyme. Such inhibitors are
U

structurally similar to the substrate, so they bind to the enzyme’s active site.
n

The substrate would be converted to a product and rele ased, le aving the

active siteopen. The inhibitor, however, becomes permanently bound to

o
d

the active site by the formation of a cov alent bond. This produces a stable

inhibitor–enzyme complex that c an never work as a c atalyst again. This is c alled

i
r

mechanism-based inhibition.
t
o

Mechanism-based inhibitors c ause harm to an organism, bec ause every molecule

a

of inhibitor c an permanently inactivate one enzyme molecule. The inhibitor may

f

kill an organism if the function of the inhibited enzyme is vital and there is a lethal
u

concentration of the inhibitor. Some living organisms synthesize a mechanism-

x

based enzyme inhibitor in order to kill another organism—for example, penicillin

l

uses this method to kill gram-positive bacteria. In addition, some chemic al

O

weapons are mechanism-based enzyme inhibitors and they are some of the most

toxic substances ever discovered.

v

O O
E

H C P N N
3

◂ Figure 34 Novichok agents are

N N mechanism-based inhibitors of the enzyme

F F

acetylcholinesterase. They are lethal in

minute quantities and have been implic ated

Novichock A-230 Novichok A-234

in some high-prole attacks on individuals

359
 Interaction and interdependence
LHA

Penicillin—an example of mechanism-based inhibition

The cell walls of bacteria prevent them from bursting when bursting (lysis). Penicillium can then monopolize the food

low external solute concentrations cause water to enter by source. The fungus only does this when food supplies are

s
osmosis and hydrostatic pressures inside the cell become limited, because resources are needed for the synthesis

very high. The enzyme transpeptidase is very important and secretion of penicillin.

s
in the process of cell wall formation, because it

Penicillium fungus

e
cross-links strands of carbohydrate into one huge

growing on the
peptidoglycan molecule that forms the entire

r
surface of the agar
cell wall. When bacteria grow, one enzyme

gel and releasing

breaks these links, allowing the wall to expand.

y
penicillin into it
Transpeptidase then remakes the links.

a few small colonies

S aprotrophic bacteria and fungi compete for

of bacteria where

l
food because they both secrete enzymes for
penicillin has diffused

n
extracellular digestion of carbon compounds
from the fungus

in dead matter and then absorb the products

through the agar gel

O
of digestion. The fungus Penicillium notatum

i
produces a chemical known as penicillin,

s
which is a mechanism-based inhibitor. It binds

to the active site of transpeptidase in the cell

y
walls of bacteria and prevents the substrate

large colonies of
e
of the enzyme from binding. Penicillin forms

p
bacteria where

a permanent covalent bond with a particular

penicillin has not

v

amino acid in the active site, binding irreversibly

reached so bacteria

o
with the enzyme. The enzyme that breaks

are not being killed

i

cross-links in the bacterial cell wall continues

n

working but the transpeptidase enzyme cannot

▴ Figure 35 Alexander Fleming’s petri dish which rst showed the inhibition
work to reform these links. As a result, the cell

of bacterial growth by penicillin from a mycelium ofPenicillium

wall is weakened and the bacteria are killed by
U

Linking questions
o
d

1. What are examples of structure–function relationships in biologic al

i
r

macromolecules?
t
o

a. Explain the relationship between allosteric enzyme shape and

a

enzyme activity. (C1.1.14)

f

b. Explain the role played by complementary base pairing in

u
x

semi-conservative replic ation. (D1.1.2)

l

c. O utline the structure of phospholipids and their role in membrane

O

structure. (B2.1.1)
a

2. What biologic al processes depend on dierences or changes in

v

concentration?
E

a. Outline the concentration changes that must occur when the axon of

a nerve is returned to resting potential. (C2.2.2)

b. Explain how H concentration c an be used to power the production

of ATP. (C1.2.15)

c. Explain how the homeostatic regulation of blood glucose

concentration c an be achieved. (D3.3.3)

360
C1.2 Cell respiration

What are the roles of hydrogen and oxygen in the release of energy in cells?

s
s
In living systems, oxidation reactions are a type of energy-releasing

reaction while reduction reactions are a type of energy-absorbing

e
reaction. Bacteria c alled methanophiles oxidize methane as an

energy source. At certain loc ations on the seabed, methane seeps

r
out from the ocean oor. As a result, a food chain c an emerge in the

y
absence oflight. In Figure 1, the white substrate is frozen methane.

The ice worms (Sirsoemethanicola) consume the bacteria that

l
grow on the methane.

n
becomes oxidized

t
▴

O
Figure 1 These ice worms (Sirsoe methanicola) are

i
at a depth of 800 m in the Gulf of Mexico
CH 2 O CO energy + 2 H O
4 2 2 2

s
r
becomes reduced

y
e

p
How is energy distributed and used inside cells?
v

Energy-rich molecules need to be converted into a usable form of energy

o
i

such as ATP. Alternatively, they c an be stored for later use in storage molecules
n

such as glycogen or starch. The breakdown of energy-rich molecules such as

glucose is done in stages, leading to the production of ATP and reduced NAD
U

and FAD. Reduced molecules transfer their electrons to the electron transport
n

chain, powering the production of more ATP. In Figure 2, the nucleus of the

parenchyma cell is surrounded by an organelle c alled an amyloplast, which

▴ Figure 2 A parenchyma cell from a

contains starch grains. M any mitochondria are also visible.

o
d

voodoo lily

SL and HL AHL only

i
r

C1.2.1 ATP as the molecule that C1.2.7 Role of NAD as a c arrier of hydrogen and oxidation by removal of hydrogen
o

distributes energy withincells during cell respiration

a

C1.2.2 Life processes within cells C1.2.8 Conversion of glucose to pyruvate by stepwise reactions in glycolysis with a
f

that ATP supplies withenergy net yield of ATP and reduced NAD
u

C1.2.3 Energy transfers during C1.2.9 Conversion of pyruvate to lactate as a means of regenerating NAD in
x

interconversions between ATP and anaerobic cell respiration

l

ADP C1.2.10 Anaerobic cell respiration in yeast and its use in brewing andbaking
O

C1.2.4 Cell respiration as a system C1.2.11 Oxidation and dec arboxylation of pyruvate as a link reaction in aerobic cell

for producing ATP within the cell respiration

v

using energy released from c arbon C1.2.12 Oxidation and dec arboxylation of acetyl groups in the Krebs cycle with a

compounds yield of ATP and reduced NAD

E

C1.2.5 Dierences between C1.2.13 Transfer of energy by reduced NAD to the electron transport chain in the

anaerobic and aerobic cell mitochondrion

respiration in humans C1.2.14 Generation of a proton gradient by ow of electrons along the electron

C1.2.6 Variables aecting the rate of transport chain

cell respiration C1.2.15 Chemiosmosis and the synthesis of ATP in the mitochondrion

C1.2.16 Role of oxygen as terminal electron acceptor in aerobic cellrespiration

C1.2.17 Dierences between lipids and carbohydrates as respiratorysubstrates

361
 Interaction and interdependence

C1.2.1 ATP as the molecule that distributes

energy within cells

adenine Nucleotides are the subunits RNA and DNA. They consist of three parts:

s
• a nitrogen-containing base
three phosphate grops

• a five-c arbon sugar

s
• one or more phosphate groups.

e
ATP is a nucleotide bec ause it consists of the base adenine, the ve-

r
c arbon sugar ribose and three phosphate groups. The phosphate

P
groups are in a chain and each of them is negatively charged.

y
ribose
ATP is oen described as the energy currency of the cell, bec ause it is

l
used for temporary storage of energy and for energy transfer between

y
▴ Figure 3 Adenosine triphosphate

n
processes and between dierent parts of the cell. The properties of ATP
(ATP). Black atoms are c arbon, oxygen

make it suitable for thisrole:

t
red, hydrogen white, nitrogen blue and

O
phosphorus yellow • ATP is soluble in water so it c an move freely through the cytoplasm

i
and other aqueous solutions in the cell.

s
• ATP is stable at pH levels close to neutral (as in cytoplasm).

y
• ATP c annot pass freely through the phospholipid bilayer of membranes. This
e
means it c annot diffuse out of a cell and its movement between membrane-

p
bound organelles within cells c an be controlled.
v

• The third phosphate group of ATP c an easily be removed and reattached by

hydrolysis and condensation reactions:

o
i
n

ATP + H O ADP + phosphate + energy

2

• Hydrolysing ATP to ADP and phosphate releases a relatively small amount

U

of energy. This is enough for many processes within the cell. If more energy
n

was released, there would often be an excess. This would be wasted by

conversion to heat.

▴ Figure 4 What are the dierences

o
d

between using c ash to buy something and

using ATP to supply energy for a process?

C1.2.2 Life processes within cells that ATP

i
r

supplies with energy

o

Cells need energy for three main types of activity.

f

1. Synthesizing macromolecules
x

Anabolic re actions that link monomers together into large polymers would
l

be endothermic and therefore unlikely to happen without coupling them

O

to conversion of ATP to ADP. One or more ATP molecules is used every

time a monomer is linked to the growing polymer. Synthesis of DNA during

v

replic ation, RNA in transcription and proteins in translation all require energy

from ATP.
E

2. Active transport

Pumping of ions or other particles across a membrane against the concentration

gradient requires energy from ATP. The energy is used to cause reversible changes

in the conformation (shape) of the pump protein. When the pump is in one

362
 Molecules

conformation, the particle can enter it from one side of the membrane. When

the pump is in the other conformation, the particle can exit on the other side of

the membrane. One of the two shapes is more stable than the other. ATP is used

to cause the change from the more stable to the less stable conformation. The

change back to the more stable conformation happens without the need for

s
energy.

s
3. Movements

e
Cells require energy from ATP for movement. Components of cells are moved—

for example, chromosomes are moved to the poles during mitosis and vesicles

r
move to transport materials within cells. L arger amounts of energy—and

therefore more ATP molecules—are needed to change the shape of a cell, for

y
example, when a dividing cell pinches apart during cytokinesis. Some cells use

changes of shape for movement from place to place (locomotion)—for example,

l
phagocytes in the human blood system move to sites of infection. Muscle cells

n
c an contract powerfully using large arrays of actin and myosin laments, which

t
exert force by sliding across each other. The energy for these movements is

O
provided by ATP.

i
s
r

y
C1.2.3 Energy transfers during e
interconversions between ATP and ADP

p
v

ATP contains more chemic al potential energy than ADP. Therefore, energy is

o
rele ase d when ATP is converte d to ADP and phosphate. The amount of energy
i

rele ase d is relatively small, but sucient for many processes within the cell.
n

In some c ases, the phosphate group is linke d to another mole cule, such as a

protein pump in the membrane or a substrate in a metabolic re action. When

the phosphate detaches from this mole cule, energy is rele ase d. This energy
U

c auses a change in the mole cule—for example, a conformational change

n

in a membrane pump or a chemic al change that converts a substrate into a

product.
o
d

Energy is required to convert ADP and phosphate back to ATP. This energy c an

come from:
i
r

• cell respiration, in which energy is released by oxidizing c arbohydrates, fats

o

or proteins
a

• photosynthesis, in which light energy is converted to chemic al energy

f

cell respiration or photosynthesis

• chemosynthesis, in which energy is released by oxidizing
x

inorganic substances such as sulfides.

l
O

The quantity of ATP within a cell at any time is very small; if it is all used

ADP +
up, processes that require energy stop. For example, neurons in the
ATP

phosphate
v

nervous system are unable to convey impulses and muscle cells stop

contracting, c ausing cramp. Without ATP, cells start to degrade within

E

minutes. This damage is soon irreparable, leading to cell death.

However, this is normally prevented by continual regeneration of ATP

active cell processes

from ADP and phosphate.

▴ Figure 5 ATP is converted to ADP + phosphate and

Energy transfers during interconversions between ATP and ADP are

back again by dierent cell processes

not 100% ecient, so some of the energy is transformed into heat.

363
 Interaction and interdependence

Activity: C alculating the rate of conversion between

ATP and ADP

s
s
e
r
P

y
l
y

n
t

O
i
s
r

y
e

p
▴ Figure 6 This six-eyed spider (Pholcus phalangioides) c an remain motionless on a
v

wall for days, conserving ATP while waiting for prey. Humans are typic ally much more

o
active, using about 120 moles of ATP per day. At any moment, there is only about
i

0.2 moles of ATP in the body. How many times per day is an average ATP molecule

converted to ADP and back again?

n

C
U

C1.2.4 Cell respiration as a system for

n

producing ATP within the cell using energy

o
d

released from c arbon compounds

Cell respiration is a function of life that is performe d by all living cells. In

i
r

respiration, c arbon compounds are oxidize d to rele ase energy and this energy
t
o

is use d to produce ATP. A wide range of c arbon compounds c an be use d as

a

respiratory substrates, but glucose and fatty acids are the main ones in many

cells. In humans, the food we e at is the source of respiratory substrates. Plants

f

use c arbohydrates or lipids previously made by photosynthesis.

x

In many cells, respiration uses oxygen and produces c arbon dioxide. It is

l
O

therefore necessary for oxygen to enter cells through the plasma membrane
a

while, at the same time, c arbon dioxide exits the cells. Together these

movements are known as gas exchange, although they do not involve direct
v

one-for-one swapping of molecules. Instead both c arbon dioxide and

oxygenmove across the plasma membrane independently, by simple diusion.

E

G as exchange and cell respiration are dierent processes but they are

interdependent. Without gas exchange, cell respiration could not continue

bec ause there would soon be a lack of oxygen and a harmful excess of c arbon

dioxide inside the cell. Without cell respiration, gas exchange could not

continue bec ause the use of oxygen and production of c arbon dioxide in

respiration cre ate the concentration gradients which c ause the gases todiuse.

364
 Molecules

Data-based questions: Energy in respiratory substrates

s
s
e
r
P

y
l
y

n
t

O
i
s
▴ Figure 7 Nutritional content of c anola (rapeseed) oil (le) and syrup (right) as shown on food labels

y
1. Compare and contrast the nutritional content of the 4. In the syrup, only the sugar contains signic ant
e

p
two foods. [3] amounts of energy. C alculate the energy content

of 100 g of sugar. [2]

v

2. The SI units for energy are joules. Using the data on

o
the syrup label, c alculate the number of kilojoules 5. Deduce whether fats or c arbohydrates are a richer
i

of energy in one kiloc alorie, giving your answer to source of energy when used as a respiratory
n

one decimal place. [1] substrate. [2]

3. The density of the c anola oil is 0.93 g per cubic

U

centimetre. C alculate the energy and fat content

n

of the c anola oil per 100 g. [2]

o
d

i
r

C1.2.5 Dierences between anaerobic and

t
o

aerobic cell respiration in humans

a

Cell respiration c an be performed using a variety of alternative metabolic

f

pathways. Some pathways are aerobic (they use oxygen). Others are anaerobic
x

(no oxygen is needed). Simple word equations summarize dierent types of cell

respiration using glucose as a substrate:

l
O

glucose + oxygen c arbon dioxide + water

Aerobic respiration in humans and
v

many other animals and plants

ADP ATP
E

Anaerobic respiration in humans, glucose lactate

other animals and some bacteria

ADP ATP

glucose ethanol + c arbon dioxide

Anaerobic respiration in yeast and

other fungi

ADP ATP

365
 Interaction and interdependence

The features of aerobic and anaerobic respiration are compared in Table 1.

Aerobic cell respiration Anaerobic cell respiration

Oxygen is used as an electron acceptor Oxygen is not used—other

in oxidation reactions substances act as oxygen acceptors

s
in oxidation reactions

s
C arbohydrates such as glucose, lipids Only c arbohydrates c an be used

e
including fats and oils and amino acids

aer deamination c an be used

r
C arbon dioxide and water are C arbon dioxide plus either lactate

wasteproducts or ethanol are the waste products;

y
water is not produced

The yield of ATP is much higher—more The yield of ATP is lower—only 2 ATP

l
y
than 30 ATP molecules per glucose per glucose

n
Initial reactions are in the cytoplasm, but All reactions happen in the

t
more occur in mitochondria including cytoplasm; mitochondria are not

O
i
use of oxygen required

s
▴ Table 1

y
In humans, the lungs and blood system supply oxygen to most organs of the
e
body rapidly enough for aerobic respiration. Sometimes, however, anaerobic cell

p
respiration is used in muscles. The advantage of anaerobic respiration is that it
v

c an supply ATP very rapidly over a short time period. It is used when we need to

maximize the power of muscle contractions.

o
i
n

In our ancestors, maximally powerful muscle contractions will have been needed

for survival by allowing esc ape from a predator or c atching prey during times of

food shortage. These events rarely occur in our lives today. Instead anaerobic
U

respiration is more likely to be used during training or sport—for example, by:

n

• weight lifters during a lift

o
d

• short-distance runners in races up to 400 metres

• long-distance runners, cyclists and rowers during a sprint finish.

i
r

L actate (lactic acid) is a waste product of anaerobic respiration in muscles. There

o

is a limit to the concentration that the human body c an tolerate and this restricts
a

how much anaerobic respiration c an be done. This is the reason for the short
f

timesc ale over which the power of muscle contractions c an be maximized. We

u
x

c an only sprint for a short distance—not more than 400 metres.

▴ Figure 8 Short bursts of intense exercise

l

Aer vigorous muscle contractions, the lactate must be broken down. This
are fuelled by ATP from anaerobic cell
O

respiration requires oxygen. It c an take several minutes for enough oxygen to be absorbed

to break down all the lactate. The demand for oxygen that builds up during a
v

period of anaerobic respiration is c alled the oxygen debt.

E

366
 Molecules

Data-based questions: Oxygen consumption in tobacco hornworms

Tobacco hornworms are the larvae of the moth Manduca plotted on separate graphs. The intermediate body mass is

sexta. L arvae emerge from the eggs laid by the adult referred to as the critic alweight.

s
female moths. There is a series of larval stages c alled
Details of the methods are given in the paper published by

instars. E ach instar grows and then changes into the next
the biologists who c arried out the research. The reference

s
one by shedding its exoskeleton and developing a new
to the research is C allier V and Nijhout H F 2011. “Control

larger one. The exoskeleton includes the tracheal tubes

e
of Body Size by Oxygen Supply Reveals Size-Dependent

that supply oxygen to thetissues.

and Size-Independent Mechanisms of Molting and

r
The graphs in Figure 9 show measurements of the Metamorphosis.” PNAS. Vol. 108. Pp 14664–14669.

respiration rate of 3rd, 4th and 5th instar larvae, made This paper is freely available on the internet at

y
using a simple respirometer. http://www.pnas.org/content/108/35/14664.full.pdf+html.

E ach data point on the graphs

l
before critical weiht aer critical weiht
shows the body mass and

n
respiration rate of one larva. For 5th instar

0.12
each instar, the results have been 0.16

O
divided into younger larvae with
0.10

i
0.14

low to intermediate body mass

s
0.08

and older larvae with intermediate

0.12

to high body mass. The results are 0.06

y
0.10

0.04
1. a. Predict, using the data
e

p
0.08
in the graphs, how the
0.02
v

respiration rate of a larva

1 2 3 4 5 6 7 8 9 10 11 12 13

o
will change as it grows from
i
1

moulting until it reaches the

nim

critical weight. [1]

0.025
0.032

4th instar
2

b. Explain the change in

O

0.030
3

respiration rate that you 0.020

U
mc / etar

0.028

have described. [2]

n

0.026

0.015

2. a. Discuss the trends in

0.024
n o i t a r ip s e r

respiration rate in larvae

o
d

0.010 0.022

above the critic al weight.

0.020

[2]
i

0.005
r

0.018
t

b. Suggest reasons for the

o

0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3 1.4

dierence in the trends

a

between the periods

0.007
f

below and above the 3rd instar

u

0.009

0.006
x

critic al weight. [2]

0.008

0.005
l

The researchers reared some

0.007
O

0.004
tobacco hornworms in air with
a

0.006

reduced oxygen content. They 0.003

0.005
v

found that the instar larvae

0.002

moulted at a lower body mass

0.004

0.001
E

than larvae reared in normal air

0.003

0.000
with 20% oxygen.
0

6
2
8

4
2
0

4 6 8
2

6
2
2
2

1
0

1
1
1

3. Suggest a reason for earlier 0 0 1 .

.

.
.

.
.

.
.

.
.

.
.

0
0

0
0
0

0
0

0
0

0 0 0

moulting in larvae reared

weiht /  weiht / 

in air with reduced oxygen

content. [2]
▴ Figure 9 Respiration rates of tobacco hornworms (C allier and Nijhout, 2011)

367
 Interaction and interdependence

C1.2.6 Exploring and designing: Variables aecting the rate of cell respiration

The rate of cell respiration c an be determined from several simple if the diameter of the space inside the tube is

types of measurement: known.

s
• oxygen uptake

C alculating rates

s
• c arbon dioxide production
A rate is an amount per unit time. Therefore, to nd the

respiration rate, the volume of oxygen used must be

• consumption of glucose or other respiratory

e
3

divided by the time. For example, if 50 mm of oxygen was

substrates.

used in ten minutes, the rate would be 5 mm oxygen per

r
Oxygen uptake is usually used to determine the rate of
minute. This calculated rate is the dependent variable in an

aerobic respiration. It c annot be measured by nding how

P
experiment using arespirometer.

y
much air is breathed into the lungs bec ause air contains

Control of variables
gases other than oxygen and only a small proportion of air

l
in each breath is absorbed by the body. Respirometers c an give accurate results but it is

n
essential to control variables c arefully. In particular,

Measuring oxygen uptake

t
temperature and pressure inside the respirometer must

O
There are many possible designs of apparatus, all known
be controlled. This is bec ause pressure, volume and

i
as respirometers. They have these parts:
temperature interact. For example, if heat generated

s
• a sealed glass or plastic container in which the
by respiring organisms increases the air temperature

organism or tissue is placed with enough air for it to

inside a respirometer, the volume of the air will increase.

y
remain healthy
If possible, temperature should be kept constant using
e
a thermostatic ally controlled water bath. If air pressure

p
• a base (alkali) such as potassium hydroxide to absorb

outside the respirometer changes, the uid in the c apillary

carbon dioxide produced during respiration
v

tube of some types of respirometer will move without any

o
• a c apillary tube containing fluid connected to the
oxygen uptake.
i

container to measure changes in the volume of air

n

Experimental investigation of variables

inside the respirometer.

Respirometers c an be used to perform experiments in

C arbon dioxide production normally adds to the volume

which one variable is deliberately changed, while all

U

of air in the atmosphere as oxygen intake reduces it. In

others are kept constant. The variable that is changed

n

a respirometer, all c arbon dioxide is absorbed by the

is c alled the independent variable. There are many

base, so any volume changes should be due to oxygen

possible experiments but they must not c ause harm to any

intake alone. Volume changes recorded by movements

o
d

organisms used. For example:

of the uid in the c apillary tube are therefore a measure of

• the respiration rate of different organisms could be

oxygen consumption.
i
r

compared
t

Converting measurements to volumes

o

• the effect of temperature on respiration rate could be

a

If the movement of the uid in the c apillary tube is

investigated

me asured in millimetres or other units of distance, it

f

• respiration rates could be compared in active and

should ide ally be converted to units of volume. This is
x

inactive organisms.
l
O

Data-based questions: Respirometers

v

Part 1: Experimental design 3. Predict, with a reason, the change in the amount of

oxygen inside the tube during the experiment. [2]

E

One possible design of respirometer is shown in

Figure 10.
4. Explain how the following changes would improve

1. Explain the need for a base inside the respirometer. [2] the reliability of results from the experiment:

2. Deduce, giving a reason, the direction in which a. putting the test tube in a thermostatic ally

the uidwill move in the right-hand side of the controlled water bath [2]

c apillarytube. [2]

368
 Molecules

7. Plot a graph of the mean volumes. [3]

8. Using your graph, deduce the relationship between

temperature and the respiration rate of the

3
graduated 1 cm germinating pea seeds. [2]

s
syringe

Part 3: Anaerobic respiration in yeast

s
The apparatus in Figure 11 was used to monitor mass

e
changes during the brewing of wine. The ask was placed
wire basket containing a

living organism or tissue on an electronic balance which was connected to a

r
filter paper rolled computer for data logging. Results are shown in Figure12.

capillary

P
to form a wick

y
tube
airlock to
potassium hydroxide

solution prevent

l
electronic
entry

n
balance
▴ Figure 10 Respirometer with a manometer for measuring
of oxygen

oxygen uptake connected

t
to a data-

O
b. attaching another test tube to the le-hand

i
logging

side of the c apillary tube, that is identic al to

yeast in a
computer

s
the right-hand tube but does not contain
solution of

respiring tissue. [2]

r
sugar and

y
nutrients

Part 2: Using secondary data

e

p
Table 2 shows the results of an experiment in which the 555.00
v

eect of temperature on respiration in germinating pea

o
seeds was investigated.
i

▴ Figure 11 Yeast data-logging apparatus

n

Temperature /°C Movement of uid in

−1
560
respirometer / mm min
U

1st 2nd 3rd

555
g / ssam
n

reading reading reading

5 2.0 1.5 2.0

550
o
d

10 2.5 2.5 3.0

15 3.5 4.0 4.0 545

i
r

20 5.5 5.0 6.0

o

0 1 2 3 4 5 6 7 8 9 10 11 12 13
a

25 6.5 8.0 7.5

time / days
f

30 11.5 11.0 9.5

u

▴ Figure 12 Monitoring anaerobic cell respiration in yeast

x

▴ Table 2

9. a. C alculate the total loss of mass during

l
O

5. D iscuss whether the repe ats at e ach temperature

theexperiment and the mean daily loss. [2]

a

are close enough to indic ate that theresults

b. Explain the loss of mass. [3]

arereliable. [1]
v

10. Suggest two reasons for the increasing rate ofmass

6. a. The diameter inside the c apillary tube of the

loss from the start of the experiment untilday 6. [2]

E

respirometer was 2 mm. Convert the distances

of movement at each temperature to volumes

11. Suggest two reasons for the mass remaining constant

of oxygen used. [2]

from day 11 onwards. [2]

b. C alculate the mean volume for each

12. Suggest how the rate of respiration c an be c alculated

temperature. [2]
from the data. [1]

369
 Interaction and interdependence

ATL Thinking skills: Designing questions for experimental investigation

To plan an investigation in biology you need a focused Consider these criteria for a good IA inquiry question:

research question. Here are some examples of research

1. The answer should not be known before starting.

s
questions involving cellrespiration in yeast.
Answering the question must depend on you c arrying

1. Which foods c an yeast use in anaerobic cell out the investigation.

s
respiration?

2. The phrasing of the question should suggest the

e
2. Which monosaccharides is yeast able to use in method to befollowed.

anaerobic cellrespiration?

r
3. The variables that are directly measured should be

3. Does yeast c arry out anaerobic cellular respiration stated in thequestion.

y
faster at 0°C or100°C?

4. The question should not include reference to

4. If oxygen is available, does yeast use aerobic or signic ance. Students oen muddle the intent of the

l
anaerobic cellularrespiration? experiment with the statement of thequestion.

n
What are some of the strengths and limitations of each 5. Consider the signic ance of your investigation to

t
question? What criteria do you think should be met for an an area that interests you. Are you interested in

O
i
inquiry question to be a goodone? alternative fuel sources, enzymesor baking bread?

s
r

y
LHA

C1.2.7 Role of NAD as a c arrier of hydrogen

e

p
and oxidation by removal of hydrogen
v

during cell respiration

o
i

Oxidation and reduction are chemic al processes that always occur together.
n

This happens bec ause they involve transfer of electrons from one substance to

another. Oxidation is the loss of electrons from a substance and reduction is the

gain of electrons.
U

adenine base
n

A useful example to help visualize this in the laboratory is in the Benedict’s test—a

test for certain types of sugar. The test involves the use of copper sulfate solution,

ribose sugar
2+ 2+

containing copper ions with a charge of two positive (Cu ). Cu ions oen
o
d

impart a blue or green colour to solutions. Sugar molecules c ause a reduction

reaction that changes these copper ions to atoms of copper by giving them
i
r

electrons. Copper atoms are insoluble and form a red or orange precipitate. The
t
o

sugar molecules are oxidized, bec ause they have lost electrons.
a

phosphates

Electron c arriers are substances that c an accept and lose electrons reversibly.
f

They oen link oxidations and reductions in cells. The main electron c arrier in
x

respiration is NAD (nicotinamide adenine dinucleotide). The structure of the NAD

molecule is shown in Figure 13.

l
O

ribose sugar
a

The equation below shows the basic reaction.

v

NAD + 2 electrons → reduced NAD

nicotinamide base
E

The chemic al details are a little more complic ated. NAD initially has one positive

charge and exists as NAD . Substances are oxidized in respiration by removing

▴ Figure 13 Structure of NAD two hydrogen atoms. E ach hydrogen consists of an electron and a proton. NAD

accepts two electrons and one proton from the hydrogen atoms, becoming

NADH. The other proton (H ) is released:

+ + +

NAD + 2H + 2 electrons (2e ) → NADH + H

370
 LHA

371
y
Molecules

s
s l
n
e
r O
P
y
y p
t
o
i
s C
r
e
n
v
o
i
n i
t
U a
u
d
l
r a
o v
f E
x
O
 Interaction and interdependence
LHA

Then there is a second phosphorylation:

fructose-6-phosphate fructose-1,6-bisphosphate

ATP ADP

s
Stage 2: Lysis

s
Fructose bisphosphate is now split to form two molecules of triose phosphate:

e
fructose-1,6-bisphosphate → 2 triose phosphate

r
Stage 3: Oxidation

P
E ach of these triose phosphates is ox i d i z e d by removing hy d r o g e n . Note

y
that hy d r o g e n atoms are remove d, not hy d r o g e n ions. If hy d r o g e n ions

were remove d (H ), no ele ctrons would h av e been lost by the triose

l
y
phosphate so it would not h av e been ox i d i z e d . The hy d r o g e n is accepted

n
by N A D, which becomes re duce d N A D. Oxidation of a sugar produces

t
an organic acid. In this c ase the sugar is triose with one phosphate
2 pyruvate

O
group and the organic acid is g l y c e ra t e c arrying two phosphates. Energy
(2 × 3C)

i
rele ase d by the ox i d a t i o n of triose a l l ows a second phosphate group to

s
become a tt a c h e d , so the product is b i s p h o s p h o g l y c e ra t e ra t h e r than

r
p h o s p h o g l y c e ra t e .
2ATP

y
NAD reduced NAD
e

p
triose phosphate + phosphate bisphosphoglycerate
v

2ADP

Stage 4: ATP formation

o
i

2ATP
n

ATP is produced in the nal reactions of glycolysis, by transfer of phosphate

groups to ADP. This c an happen twice bec ause bisphosphoglycerate has two

phosphates. In these reactions, the glycerate is converted to another organic

U

2 reduced NAD
acid, pyruvate. This is the end product of glycolysis.
n

2ADP

bisphosphoglycerate pyruvate
o
d

ADP ATP ADP ATP

2NAD

ADP Two bisphosphoglycerate molecules are produced per glucose and each of
i
r

them yields two ATPs. Four ATPs are therefore produced per glucose in these
t
o

nal reactions of glycolysis.

a

The overall outcomes of the four stages of glycolysis per glucose molecule are
f

ATP
u

asfollows:

ADP
x

• One glucose containing six c arbon atoms is converted into two pyruvates
l

each containing three c arbon atoms.

O

• Two NAD molecules are converted to reduced NAD.

ATP
v

• There is a net yield of two ATP s. This is be c ause two are use d in the first

stageof glycolysis and four are produce d in the final stage, so the net
glucose
E

yield is 4 − 2 = 2 per glucose. Although this is a relatively small yield, it

(6C)

does not re quire the use of oxygen so is useful when the supply of oxygen

▴ Figure 14 An overview of glycolysis islimite d.

372
 Molecules

LHA
C1.2.9 Conversion of pyruvate to lactate as

a means of regenerating NAD in anaerobic

cellrespiration

s
The summary equation for glycolysis (Figure 14) shows that supplies of glucose,

ADP and NAD must be replenished for the process to continue in a cell.

s
H C O H

• Glucose should not run out as long as there are stores in a cell or it is

e
transported from elsewhere.
H
C C

r
• ADP will only run out if all of it has been converted to ATP, in which c ase there

H
is no need to c arry out glycolysis.
O

y
• NAD will run out unless it is regenerated by oxidation of reduced NAD.

▴ Figure 15 This is pyruvic acid. It readily

l
There are several methods of regenerating NAD. In each c ase, two hydrogen +

gives up a proton (H ) from the hydrogen

y
atoms (two protons and two electrons) are transferred to another molecule,

n
atom shown on the right-hand side,

oxidizing reduced NAD. In some human cells and also some other animal
keeping the electron from the hydrogen. It

t
and bacterial cells, hydrogen is transferred from reduced NAD to pyruvate, is then pyruvate, with one negative charge.

O
Pyruvate c an accept a proton to become
converting it into lactate. This happens in the cytoplasm of cells.

i
pyruvic acid. Organic acids such as pyruvic

s
pyruvate lactate
acid and lactic acid normally exist in their

r
dissociated state, so are referred to with the

y
NAD reduced NAD
‘–ate’ name rather than the ‘–ic acid’ name
e
Two NAD molecules are used as each glucose is converted by glycolysis to

p
pyruvate. Two pyruvates are produced and each of them c an be used to convert
v

a reduced NAD back to NAD, so all the NAD that was used in glycolysis is

regenerated. For this reason, cells should not run out of NAD: as long as glucose
o
i

is available and lactate concentrations do not rise too high, anaerobic cell
n

respiration c arried out in this way should be able to continue indenitely.

U

Anaerobic cell respiration by glycolysis with conversion of pyruvate to lactate

is c alled lactic fermentation. It is used in some methods of food preservation,

n

bec ause an accumulation of lactic acid (which dissociates to form lactate) lowers

the pH and prevents decomposition by bacteria or fungi. Yoghurt, kimchi,

o
d

sauerkraut and silage (for c attle) are all foods made by lactic fermentation.
i
r

▴ Figure 16 Kimchi was traditionally made

o

C1.2.10 Anaerobic cell respiration in yeast

from c abbage and other vegetables in
a

South Korea, using large underground pots.

and its use in brewing and baking
f

It provided food for the winter when fresh

u

NAD used in glycolysis can be regenerated by conversion of pyruvate to ethanol

vegetables were not available. The cool
x

and carbon dioxide instead of lactate. This is a two-stage process. In the rst
anaerobic conditions in the pots encourage
l

stage, carbon dioxide is removed from the pyruvate in a decarboxylation reaction. Lactobacillus and other bacteria to c arry
O

The product is ethanal. In the second stage, two hydrogens are transferred out lactic fermentation, eventually killing

themselves with low pH and preserving

from reduced NAD to ethanal, converting it to ethanol. The number of NADs
v

thevegetables
regenerated is the same as the number used per glucose in glycolysis, so this

process allows production of ATP by anaerobic respiration to continue indenitely,

E

as long as glucose is available and ethanol concentrations do not rise too high.

ethanal

CO reduced NAD
2

NAD

▴ Figure 17 Conversion of pyruvate to ethanol

373
 Interaction and interdependence
LHA

Anaerobic cell respiration by glycolysis which converts pyruvate to ethanol and

c arbon dioxide is known as ethanol fermentation or alcoholic fermentation. It

is used in baking and brewing. In both c ases, the organism that c arries out the

fermentation is yeast. Yeast is a unicellular fungus that occurs naturally in habitats

where glucose or other sugars are available, such as the surface of fruits. Yeast is a

s
faculative anaerobe—this means it c an respire either aerobic ally or anaerobic ally.

s
Bread is made by adding water to our, kneading the mixture to make dough

e
and then baking it. To give the bread a lighter texture, something must be added

to the dough to create bubbles of gas. Yeast is oen used for this purpose. If the

▴ Figure 18 Kneading mixes the

r
dough is kept warm, the yeast will grow and respire. Initially it respires aerobic ally

ingredients and stretches out gluten bres,

but once all the oxygen in the dough has been used up, the yeast starts to respire

P
making bread dough more elastic

y
anaerobic ally. Bec ause the dough is very viscous (sticky), the c arbon dioxide

produced by anaerobic cell respiration c annot esc ape. Instead, it forms bubbles

l
within the dough. These bubbles c ause the dough to swell, or “rise”. Ethanol is

n
also produced by anaerobic cell respiration but it evaporates during baking.

t
Ye ast is also used when brewing drinks such as beer and wine. Here, however,

O
the aim is to produce ethanol rather than c arbon dioxide. Wine is made from

i
grape juice, which naturally has a high sugar concentration. Beer is made from

s
barley grains, mixed with water. The grains contain large amounts of starch but

r
little sugar. This starch must rst be converted to sugar using amylase, bec ause

y
ye asts c annot metabolize starch. Brewing of wine or beer is c arried out in large
e

p
tanks, so diusion of oxygen into the liquid in the tank is limited. The ye asts

▴ Figure 19 Brandy that is burned on

rapidly use up any oxygen present and then respire anaerobic ally. The ethanol
v

fruit puddings in some countries is distilled

produced remains dissolved but most of the c arbon dioxide bubbles to the

from wine. What does the release of heat

surface and esc apes. Depending on the
o amount of sugar present at the start,
i

by the ame tell us about ethanol as a waste

ethanol fermentation ends either when all the sugar has been used uporwhen
n

product of anaerobic cellrespiration?

the ethanol concentration becomes toxic to the ye ast (about 15%by volume).
U

As well as brewing drinks, ethanol fermentation c an also be used to produce

n

bioethanol, a renewable energy source. Any plant matter c an be utilized as a

feedstock, but most bioethanol is produced from sugar c ane and corn (maize),

using yeast. Sugars are converted into ethanol in large fermenters. The ethanol
o
d

is puried by distillation. Bioethanol is used as a fuel in vehicles, sometimes in a

pure state and sometimes mixed with gasoline(petrol).

i
r

t
o

C1.2.11 Oxidation and dec arboxylation

f

of pyruvate as a link reaction in aerobic

x

cellrespiration
l
O

If oxygen is available, pyruvate c an be oxidized to c arbon dioxide and water.

This gives a much higher yield of ATP than anaerobic cell respiration. Most of
v

the reactions are part of the Krebs cycle, but an initial reaction is conversion of

pyruvate from glycolysis into a two-c arbon acetyl group. This conversion forms a
E

link between glycolysis and the Krebs cycle, so is referred to as the link reaction.

▴ Figure 20 Bioethanol is currently an

In the link reaction a complex of three enzymes c arries out these processes:

alternative to fossil fuels. What is the best

• dec arboxylation by removal of c arbon dioxide, to change three-c arbon

energy source for cars in a zero-carbon future?

pyruvate into a two-c arbon molecule

• oxidation by removal of two electrons; these electrons are accepted by NAD,

converting it to reduced NAD

374
 Molecules

LHA
• binding of the acetyl group (produced by the previous two process) to

a complex c arrier molecule c alled coenzyme A. The product is acetyl

coenzyme A.

CoA

s
CoA
inner
outer

s
membrane
membrane

e
r
CH CH
3 3

CO NAD+ reduced NAD

2

y
▴ Figure 21 The link reaction

l
Pyruvate is produced by glycolysis in the cytoplasm, but both the link reaction

y
matrix

n
and the Krebs cycle take place in the matrix of the mitochondrion. A transporter inter-

protein in the outer membrane of the mitochondrion moves pyruvate from the membrane

O
cytoplasm into the mitochondrial matrix. space

i
▴ Figure 22 Membranes and

s
compartments of a mitochondrion

r
C1.2.12 Oxidation and dec arboxylation of

y
e
acetyl groups in the Krebs cycle with a yield

p
of ATP and reduced NAD
v

Acety l groups produce d by the link re action are oxidize d in a cycle of

o
i

re actions that happens in the matrix of the mitochondrion. This cycle has
n

several names but is commonly c alle d the “Krebs cycle” in honour of the

biochemist who w as aw arde d a Nobel Prize for its discovery. Acety l groups
U

are fe d into the cycle by transfer from coenzyme A to oxaloacetate, producing

n

the organic acid citrate.

acetyl CoA

Oxaloacetate has four c arbon atoms and

o
d

oxaloacetate citrate
citrate has six. Citrate is converted back into

6C
4C
oxaloacetate by a series of enzyme-c atalysed

reduced NAD
i
r

re actions. The number of c arbon atoms is

t

decre ased by two dec arboxylation re actions, NAD

o

6C

in which c arbon and oxygen are removed,

a

4C
producing c arbon dioxide. In aerobic cell
CO
2
f

NAD

respiration, all the c arbon in substrates such

u

Krebs cycle
x

as sugar or fat is removed by dec arboxylation

reduced NAD
H O
2

in the Krebs cycle or the link re action. C arbon

l

4C
O

dioxide is a waste product in most cells and is 5C

a

CO
2
excreted.
v

Four re actions in the Krebs cycle are oxidations

reduced FAD NAD

and rele ase energy. Much of the rele ased 4C

4C
E

FAD

reduced NAD
energy is held by the electrons that are

removed in the oxidations. These electrons are

ATP
ADP

transferred either to NAD or to FAD. Both these

▴ Figure 23 The Krebs cycle

molecules act as c arriers of electrons; they also

accept protons, so they are hydrogen c arriers

375
 Interaction and interdependence
LHA

as well. NAD was described e arlier in this topic. FAD functions in a similar way.

When FAD or NAD accept a pair of electrons, they become reduced. Reduced

NAD and reduced FAD transfer electrons and the energy they are holding to

the electron transport chain in the inner mitochondrial membrane.

s
The net eects of one turn of the Krebs cycle are:

• one acetyl group is consumed

s
• three NADs are converted to reduced NAD and one FAD to reduced FAD

e
• two molecules of c arbon dioxide are released

r
• one ADP is converted to ATP.

y
Activity: Turns of the cycle

l
y
Discuss the answers to these questions with your classmates:

n
acetyl group

1. Two c arbon dioxide molecules are released for each acetyl

t
group fed into the Krebs cycle. How many c arbon dioxide

O
i
molecules are produced by the cycle for each glucose?

s
2. Linoleic acid is the commonest fatty acid in sunflower oil. It has

18 c arbon atoms that are c atabolized into 9 two-c arbon acetyl

y
CO
2

groups during aerobic respiration. How many molecules

e
of c arbon dioxide are released by the Krebs cycle when a

p
molecule of linoleic acid is used in aerobic respiration?
v

3. The maze diagram in Figure 24 represents the route of c arbon CO

o
2
i

atoms through the Krebs cycle. C an you explain it?

n

C
U

▴ Figure 24
n

C1.2.13 Transfer of energy by reduced

o
d

NAD to the electron transport chain in

i
r

themitochondrion
t
o

In the inner mitochondrial membrane, there are groups of proteins that act as

electron c arriers by accepting and then passing on pairs of electrons (see Figure
f

25). Together, this sequence of c arriers forms the electron transport chain (ETC).
x

The rst c arrier in the chain accepts a pair of electrons from reduced NAD. This

changes the c arrier from an oxidized state to a reduced state and converts the
l
O

reduced NAD back to NAD. The c arrier gains chemic al energy by this transfer of
a

electrons.
v

Reduced NAD is produced in glycolysis, the link reaction and the Krebs cycle.

Oxidation reactions in these processes are the source of the energy that is
E

transferred by reduced NAD to the ETC. The Krebs cycle also produces reduced

FAD, which transfers a pair of electrons to the ETC. The electrons transferred

by reduced FAD c arry less energy than those from reduced NAD, so they are

accepted by a c arrier part way along the chain which has a higher anity for

electrons than the rst c arrier.

376
 Molecules

LHA
Reduced NAD from glycolysis

enters the mitochondrion.

Reduced NAD transfers

electrons carrying energy

s
to electron transport chains

in the inner mitochondrial

s
membrane. Infoldings of this

e
membrane called cristae

increase the area of membrane

r
and the number of ETCs it can

accomodate.
Reduced NAD is produced in the matrix

y
of the mitochondrion by the link reaction

and rebs cycle. It only has a short distance

l
to trael to reach the inner mitochondrial

n
membrane.

t
▴ Figure 25

O
i
s
C1.2.14 Generation of a proton gradient

y
byow of electrons along the electron
e

p
transport chain
v

o
Electrons brought to the inner mitochondrial membrane by reduced NAD are
i

accepted by the rst c arrier in the electron transport chain. They then pass

along the chain from c arrier to c arrier. Energy is rele ased at every stage in this
n

ow ofelectrons.
U

The thre e main c arriers in the ele ctron transport chain e ach act as proton
n

pumps. They use energy rele ase d by the ow of ele ctrons to pump

protons ac ross the inner mitochondrial membrane, f rom the matrix to the

intermembrane space betwe en the inner and outer mitochondrial membranes.

o
d

The rst and se cond main ele ctron c arriers e ach pump four protons per pair

of ele ctrons; the third c arrier pumps two. This gives a total of 10 protons
i
r

pumpe d f rom the matrix to the intermembrane space per pair of ele ctrons
t
o

from re duce d NAD.

a

Electrons brought by reduced FAD also fuel proton pumping. However, these
f

electrons are fed into the chain aer the rst c arrier so only 6 protons are pumped
x

per pair of electrons, rather than 10.

l

Energy
O

is needed to pump protons across the inner mitochondrial membrane

a

bec ause they are being moved against the concentration gradient. This energy

is not lost—it is stored temporarily in the form of the proton gradient. This stored
v

▴ Figure 26 Energy is required to

energy c an then be used to generate ATP.

pump water up to the tank at the top of

E

In summary, the role of the electron transport chain is to generate and maintain
a water tower. What are the similarities

a proton gradient across the inner mitochondrial membrane. It does this by and dierences between this and proton

pumping protons across the membrane using energy released by the ow of pumping in the mitochondrion?

electrons. The electrons from which this energy is obtained are brought to the

ETC by reduced NAD and reduced FAD.

377
 Interaction and interdependence
LHA

C1.2.15 Chemiosmosis and the synthesis of

ATP in the mitochondrion

ATP synthase is a large and complex protein that phosphorylates ADP to produce

ATP. This is an endergonic (energy absorbing) reaction so a source of energy is

s
needed. This energy is provided by the proton gradient created by the electron

s
transport chain. The process used to couple the proton gradient to synthesis of

ATP is c alled chemiosmosis.

e
In osmosis, a concentration gradient c auses water to move across a membrane,

r
but the energy released by this process is not utilized. In chemiosmosis, protons

P
move down their concentration gradient from the high concentration in the

y
intermembrane space to the lower concentration in the matrix. The energy
▸ Figure 27 M any cristae are visible

released is used to link a phosphate group to ADP, producing ATP.

in this electron micrograph of a

l
y
mitochondrion. Cristae are infoldings of

n
ATP synthase has two main regions. One of these is made of transmembrane
the inner mitochondrial membrane. The

subunits that are embedded in the inner mitochondrial membrane. This region
small blobs visible on some of the cristae

O
allows protons to pass across the membrane, releasing energy. The other main
are the globular part of ATP synthase that

i
projectsfrom the membrane region is globular and projects into the matrix. It has active sites that use energy

s
(M agnic ation ×73,000) released by the protons to c atalyse production of ATP.

y
e
ATL Communic ation skills: Creating biologic al diagrams

p
v

Examine the electron micrograph of a mitochondrion dicult to distinguish detail or to identify what a label

o
in Figure 27. Create your own drawing of the is pointing to.
i

mitochondrion. Consider the following guidelines

• Draw structures in proportion to one another—for

n

regarding biologic al drawings.

example, do not draw the mitochondrial cristae

• Leave no gaps in the lines when drawing closed

too thickly, the ribosomes too large, or the

shapes.
U

intermembrane space too wide.

n

• Include clear and unambiguous labels.

• Ensure every line has meaning. For example, do not

draw a line across the base of the cristae—this would

• Ensure the size of the diagram is proportional to its
o
d

suggest that they are partitioned o from other parts

complexity. If your drawing is too small, it will be

of the intermembrane space.

i
r

t
o

Activity: Evaluating and annotating a diagram of a mitochondrion

f

Consider this student drawing of a mitochondrion. 2. Look at the structures labelled A, B, C and D. State:
x

a. the function of structure A

l

A
O

B b. the loc ation where protons build up as a result of

a

C
the electron transport chain

D
v

c. the loc ation of the enzyme ATP synthase

d. which letter indic ates the matrix

E

▴ Figure 28

e. which letter indic ates the cristae

1. What feedback would you oer to the student

regarding their drawing? f. which letter indicates the intermembrane space.

378
 Molecules

LHA
δ

matrix of
α
ATP
α
β

mitochondrion

s
s
b γ
2

e
+ inner mitochondrial
H

r
H
+
+
+ membrane
H H
H

c
c c

y
a

intermembrane

l
space

n
◂ Figure 29 The structure of ATP synthase

t
Chemiosmosis—the mechanism used by ATP synthase to make ATP—has only

O
i
been understood in recent years. Some details are given here, using letters to

denote the parts of ATP synthase.

s
• The drum-shaped part of ATP synthase loc ated in the membrane consists

y
of identic al subunits (c), each of which has a binding site for a proton.
e Next

to this is another structure in the membrane (a) with two half-channels for

p
protons. One of these half-channels allows protons from the intermembrane
v

space to enter and bind to a subunit of the drum. The other half-channel

o
allows protons that were bound to a subunit to exit to the matrix. These
i

two half-channels are not aligned so, for protons to pass through, the drum
n

has to rotate. The energy released by movement of protons down their

concentration gradient is transformed into kinetic energy. E ach proton is

c arried by the drum for almost a full rotation before it is released.

U

• The drum is tightly connected to a stalk (γ) that projects into the matrix. Because
n

of the tight connection, rotation of the drum causes the stalk to rotate at the

same rate. The drum and stalk together are known as the rotor of ATP synthase.
o
d

• The stalk is surrounded by the globular part of ATP synthase, which consists

of a ring of alternating subunits ( α and β). E ach of the β subunits has an active
i
r

site for c atalysing the phosphorylation of ADP to ATP. When the stalk inside
t
o

the ring of α and β subunits rotates, it c auses conformational changes to the

a

β subunits. These changes first c ause ADP and a phosphate group to bind to

the active site; then they c ause the phosphate to link to the ADP to produce
f

ATP; and finally they c ause the ATP to be released into the matrix. This is how
x

rotation of the stalk provides energy for ATP production.

l

• Rotation of the ring of α and β subunits is prevented by a structure adjacent

O

to it c alled the rotor arm. This consists of two parts (b and δ) linked to the
2

proton channel (a).

v

With an understanding of how ATP synthase works, we c an predict rates of ATP

production per reduced NAD and per reduced FAD:

E

• Three β subunits in ATP synthase each make one ATP per turn of the rotor.

• One proton must pass through each of the 10 c subunits in the rotor of ATP

synthase to c ause one rotation.

• Each pair of electrons from reduced NAD that passes along the ETC results in ten

protons pumped into the intermembrane space, and each pair of electrons from

reduced FAD results in pumping of six protons.

• Production of ATP is therefore 2.5per reduced NAD and 1.5 per reduced FAD.
379
 Interaction and interdependence
LHA

C1.2.16 Role of oxygen as terminal electron

acceptor in aerobic cell respiration

ATP production by mitochondria c an only continue when there is electron

ow and proton pumping. This depends on reduced NAD supplying pairs of

s
electrons to the start of the electron transport chain and the electrons being

s
removed at the end of the chain. E ach electron c arrier in the ETC has a stronger

anity for electrons than the previous one, so removal of electrons from the last

e
electron c arrier c an only be done by a substance that has a very strong anity for

electrons. Most organisms use molecular oxygen for this purpose. It is known as

r
the terminal electron acceptor. Molecules of oxygen accept electrons from the

y
nal electron c arrier and hydrogen ions from the matrix, producing water.

Use of oxygen is the last stage in aerobic cell respiration. However, all the

l
▴ Figure 30 Cryo-electron microscopy previous stages apart from glycolysis depend on oxygen. If oxygen runs out,

n
allows generation of detailed images of
electrons are not removed from the end of the ETC, so all the c arriers in the ETC

ATPsynthase

t
become reduced. This means electrons c annot be accepted from reduced NAD

O
at the start of the ETC. Reduced NAD therefore accumulates. When all the NAD

i
in the mitochondrion has been converted to reduced NAD, oxidations in the

s
link reaction and Krebs cycle are impossible so these processes stop. Anaerobic

r
cell respiration c an continue in the cytoplasm by regenerating NAD without

y
using oxygen. However, the yield of ATP is far smaller—only 2 ATP per glucose,
e
compared with 32 from aerobic cellrespiration.

p
v

inner inter

mitochondrial membrane
o
i

matrix membrane space

n

▴ Figure 31 Mitochondria in humans

U

reduced NAD

produce about half a litre of water per day +

n

2H

as oxygen combines with electrons from the +

NAD
‒
2e
ETC and protons from the matrix

2H
o
d

reduced FAD
i
r

2H
t
o

FAD

Activity: Interpreting
a

a diagram
f

H 
2
u

2H
x

Examine the diagram of

+ +

2H 2H

interactions in the inner

l

2
‒
O


mitochondrial membrane
a

(Figure32). Deduce the eect of 

the production of water on the

v

+
concentration gradient across the
10H
E

membrane.

3ATP 3ADP

+ +
low H high H ◂ Figure 32 Interactions in the

concentration concentration inner mitochondrial membrane

380
 Molecules

LHA
Data-based questions: Water production in kangaroo rats

K angaroo rats are small mammals that live in arid habitats kangaroo rat Dipodomys spectabilis, which lives in Mexico

where no water is available to drink and the foods eaten are and the south west of the US. All the values are shown per

−1

s
mainly dry seeds. Table 3 gives experimental data for the gram of food consumed (g ).

s
Food Metabolic water Oxygen used Dry air (20% relative Humid air (66% relative

type production / g in respiration/ humidity) humidity)

e
−1 3 −1

eaten water g food cm g

Evaporative Net water Evaporative Net water

r
−1 −1

water loss / yield / g g water yield / g g

−1 −1

g g loss / g g

y
starch 0.556 828 0.472 0.084 0.270 0.286

l
sugar 0.600 746 0.425 0.175 0.243 0.357

n
lipid 1.071 2019 1.151 −0.080 0.658 0.413

protein 0.396 967 0.551 −1.613 0.315 −1.377

O
i
Source of data: Frank, C. 1988. “Diet Selection by a Heteromyid Rodent: Role of Net Metabolic Water Production”. Ecology. Vol. 69.

Pp 1943–1951

s
▴

r
Table 3

y
e
1. a. Distinguish between metabolic water production

p
when the substrate for cell respiration is
v

c arbohydrate or lipid. [2]

o
i

b. Explain the dierence in metabolic water

production. [2]
n

2. a. Distinguish between the amount of oxygen

U

usedwhen the substrate for cell respiration

is c arbohydrate or lipid. [2]

n

b. Explain the dierence in the amount of

o

oxygenused. [2]
d

3. The kangaroo rats lost water by evaporation

i
r

at dierent rates in dry and humid air. Explain

t

howairhumidity aects rates of evaporative

o

waterloss. [2]
a

▴ Figure 33 K angaroo rat

f

4. Evaluate the food types, using the data in

u

Table 3. [3]
x

5. The kangaroo rats are nocturnal. Suggest

l
O

advantages of this, using the data in Table 3. [2]

a
v
E

381
 Interaction and interdependence
LHA

C1.2.17 Dierences between lipids and

c arbohydrates as respiratory substrates

Both lipids and c arbohydrates c an be used as substrates in respiration. This is why

they are both suitable as energy-yielding foods in the diet and also as energy stores

s
in the body. Both lipids and c arbohydrates are oxidized in respiration to release

s
energy. However, there are dierences in the metabolic pathways and in the

energy yield per gram. These are shown in Table 4.

e
r
◂ Figure 34 A traditional doughnut has a mass of 46 grams and contains 11.0 grams of fat

and 18.6 grams of c arbohydrate. Does the fat or the c arbohydrate provide moreenergy?

y
l
y
C arbohydrates Lipids

n
Is anaerobic The rst stage of respiration with sugars such as glucose The rst stage of respiration with lipids such

t
respiration and fructose as the substrate is glycolysis, which as fats and oils is the breakdown of fatty

O
i
possible? generates some ATP and does not require oxygen. acids to acetyl groups in the matrix of the

Anaerobic respiration is therefore possible. mitochondrion. The acetyl groups are then

s
Pyruvate can be converted to acetyl groups by the link fed into the Krebs cycle. These stages only

r
reaction and the acetyl groups can then be fed into the happen when oxygen is available, so anaerobic

y
Krebs cycle. These stages can only happen if oxygen is respiration is not possible with lipids.
e

p
available.
v

What is The energy yield per gram of c arbohydrate is only 17 The energy yield per gram of lipids is 37

o
the energy kilojoules per gram. This is about half that from lipids. kilojoules per gram. This is nearly twice as much
i

yield? Energy is released from a substrate by oxidizing c arbon as that from c arbohydrates. Nearly 90% of the
n

and hydrogen and in c arbohydrates more than 50% of mass of lipids is c arbon and hydrogen, from

the mass is oxygen, which does not yield energy. which there is a yield of energy in respiration.
U

Linking questions
▴ Table 4

1. In what forms is energy stored in living organisms?

o
d

a. Explain the concepts of primary and secondary production.

i

(C4.2.15)
r

b. Outline the use of polysaccharides as energy storage molecules in

o

animals and plants. (B1.1.5)

f

c. Describe the production of ATP by chemiosmosis in the

u

mitochondrion. (C1.2.15)
x

2. What are the consequences of respiration for ecosystems?

l
O

a. Outline how carbon dioxide enrichment experiments have been used

to predict future rates of photosynthesis and plant growth. (C1.3.8)

v

b. Explain how the process of cellular respiration sets limits to the length

of food chains. (C4.2.12)

E

c. Describe an experiment to measure a variable affecting the rate of

production of CO as a result of cellular respiration. (C1.2.6)

2

382
 Molecules

LHA
Data-based questions: Cellular respiration in shaker

muscles

The end of the tail of a rattlesnake consists of a series of hollow, interlocked

s
segments made of keratin, which are created by modifying the sc ales that

s
cover the tip of the tail. The rattle serves as a warning to predators. The

contraction of special “shaker ” muscles in the tail c auses these segments to

e
vibrate against one another, resulting in the rattling noise. Table 5 shows the

results of continuous stimulation of the tailshaker muscle of eight western

r
diamond rattlesnakes (Crotalus atrox).

y
l
y

n
t

O
i
▴ Figure 35 Western diamond rattlesnake (Crotalus atrox)

s
O content in L actate content in

r
2

y
−3 −3

arteries / mmol dm arteries / mmol dm

e

p
At rest 2.4 ± 0.5 2.8 ± 1.2
v

R attling 2.8 ± 0.1 4.8 ± 0.8

o
i

▴ Table 5
n

The graph in Figure 36 shows ATP demand and sources of ATP supply in the

tailshaker muscle.
U

Key
n

ATP from chemiosmosis

dnamed dna ylppus fo

ATP from glycolysis

s

2.0
o
3

ATP demand
md

1.5
lomm / PTA

i
r

Source: Kemper, W.F. et al.

t

1.0
o

(2000) “Shaking up glycolysis:

a

Sustained, high lactate ux

0.5 during aerobic rattling,”

f
r of
etar

Proceedings of the National

u

Ac ademy of Sciences, 98(2),

x

0.0

pp. 723–728. Available at:

ATP ATP

https://doi.org/10.1073/
l

supply demand
O

pnas.98.2.723
a

▴ Figure 36
v

1. Using the bar chart, determine the amount of ATP produced by

chemiosmosis, giving the units. [1]

E

2. Compare the changes in oxygen and lactate content in the blood

when a resting rattlesnake starts rattling. [2]

3. Using the data, deduce, with reasons, whether anaerobic respiration

provides some or all of the ATP used in rattling. [3]

4. Comment on the variability of the data. [2]

383
 C1.3 Photosynthesis

How is energy from sunlight absorbed and used in photosynthesis?

s
s
Light energy is absorbed by pigments that transform and

transfer the energy to a complex system of molecules

◂ Figure 1 A

e
known as photosystems. The molecular model shown molecular model

represents photosystem II. These are collections of photosystem,

r
which absorbs
of proteins found on the thylakoid membranes of

P
lightand uses the

y
cyanobacteria, algae and plants. They use the energy from

energy to drive the

light to reduce other molecules. What is the mechanism by

oxidation of water,

l
which they achieve this? The nal products of the activities

creating oxygen as

n
of the photosystems is ATP and NADP. How are these

a by-product

used to produce c arbohydrates?

O
i
s
How do abiotic factors interact with photosynthesis?

y
e
Abiotic factors that inuence the rate of

p
photosynthesis include: the availability of raw
v

materials such as c arbon dioxide; the amount of

o
light; the availability of mineral nutrients; and climate
i

factors such as temperature and precipitation.

n

Antarctic a’s freezing temperatures, poor soil quality,

lack of sunlight and frozen water restrict rates of

photosynthesis. L arge plants are therefore absent.

U

In areas where the snow melts during the short

n

summer, only algae, mosses, lichens and fungi grow. ▴ Figure 2

o
d

SL and HL AHL only

C1.3.1 Transformation of light energy to chemic al energy C1.3.9 Photosystems as arrays of pigment molecules that
i
r

when c arbon compounds are produced in photosynthesis c an generate and emit excited electrons
t
o

C1.3.2 Conversion of c arbon dioxide to glucose in C1.3.10 Advantages of the structured array of dierent
a

photosynthesis using hydrogen obtained by splitting water types of pigment molecules in a photosystem

C1.3.3 Oxygen as a by-product of photosynthesis in plants, C1.3.11 Generation of oxygen by the photolysis of water in
f

algae and cyanobacteria photosystem II

x

C1.3.4 Separation and identication of photosynthetic C1.3.12 ATP production by chemiosmosis in thylakoids
l

pigments by chromatography C1.3.13 Reduction of NADP by photosystem I

O

C1.3.5 Absorption of specic wavelengths of light by C1.3.14 Thylakoids as systems forperforming the light-

photosynthetic pigments dependent reactions ofphotosynthesis

v

C1.3.6 Similarities and dierences of absorption and action C1.3.15 C arbon xation by Rubisco

spectra C1.3.16 Synthesis of triose phosphate using reduced

E

C1.3.7 Techniques for varying concentrations of c arbon NADP and ATP

dioxide, light intensity or temperature experimentally to C1.3.17 Regeneration of RuBP in the C alvin cycle using ATP

investigate the eects of limiting factors on the rate of C1.3.18 Synthesis of c arbohydrates, amino acids and other

photosynthesis c arbon compounds using the products of the C alvin cycle

C1.3.8 C arbon dioxide enrichment experiments as a means and mineral nutrients

of predicting future rates of photosynthesis and plantgrowth C1.3.19 Interdependence of the light-dependent and light-

independent reactions

384
 Molecules

C1.3.1 Transformation of light energy to

chemic al energy when c arbon compounds

are produced in photosynthesis

s
Living organisms require complex c arbon compounds to build the structure of

their cells and to c arry out life processes. Some organisms are able to make all

s
the c arbon compounds they need using only light energy and simple inorganic

e
substances such as c arbon dioxide and water. They do this using the process

ofphotosynthesis.

r
Photosynthesis is an energy conversion, as light energy is converted into chemical

y
energy in carbon compounds. The main groups of carbon compounds produced

are carbohydrates, proteins, lipids and nucleic acids. This transformation supplies

l
most of the chemical energy needed for life processes inecosystems.

n
t

O
C1.3.2 Conversion of c arbon dioxide to

i
s
glucose in photosynthesis using hydrogen

▴ Figure 3 The trees in one hectare of

r
obtained by splitting water

y
redwood forest in C alifornia c an have a

biomass of more than 4,000 tonnes. Most

e
Plants convert c arbon dioxide and water into c arbohydrates by photosynthesis.

p
of this mass is c arbon compounds produced

The simple equation below summarizes the process, with glucose as the

by photosynthesis
v

c arbohydrate produced:

o
i

c arbon dioxide + water → glucose + oxygen

n

Hydrogen is needed for the reduction reaction that converts c arbon dioxide into

glucose. This hydrogen comes from photolysis (a reaction that splits molecules
U

of water). This reaction only happens when light is available to provide energy:
n

“photo” means light and “lysis” means to make loose. Hydrogen is released from

water as separated protons (hydrogen ions) and electrons.

o
d

2H O → 4e + 4H + O
2 2
i

Oxygen is a waste product of this reaction. It diuses out of photosynthesizing cells.

r

t
o

a
f

u
x

l
O

a
v
E

▴ Figure 4 Leaves absorb c arbon dioxide and light and use them in photosynthesis

385
 Interaction and interdependence

C1.3.3 Oxygen as a by-product of

photosynthesis in plants, algae and

cyanobacteria

s
Oxygen is a by-product of photosynthesis, usually a waste product. It comes from

the splitting of water (photolysis). Prokaryotes were the rst organisms to perform

s
photosynthesis, starting about 3,500 million years ago. Millions of years later,

e
algae and plants also began c arrying out photosynthesis using chloroplasts.

r
Photolysis increases the concentration of oxygen inside chloroplasts. This c auses

oxygen to diuse out of chloroplasts and then out of leaf cells to air spaces inside

y
the leaf. The oxygen then diuses through stomata to the air outside the leaf.

l
y

n
t

O
i
s
r

y
e

p
v

o
i

▴ Figure 5 Oxygen produced by photosynthesis diuses out through the stomata of

leaves. This c annot be seen with leaves in the air but bubbles are sometimes visible on leaves
n

of underwater plants when the water is saturated with oxygen

U

Water, water everywhere

All the oxygen that diuses into the air from plant leaves, or emerges as
o
d

bubbles from aquatic plants, comes from photolysis. For each glucose

molecule that is produced, 12 water molecules are split giving 24 hydrogen

i
r

ions. Figure 6 shows why so much hydrogen is needed to produce one

t

molecule ofglucose.
o

6CO + 12H O + light C H O + 6O + 6H O

2 2
6 12 6 2 2
f

u
x

l
O

a
v
E

▴ Figure 6

386
 Molecules

C1.3.4 Experimental techniques: Separation and identic ation of

photosynthetic pigments by chromatography

Chloroplasts contain several the strip and allow it to dry before adding another

s
types of chlorophyll, along drop. Repeat as many times as necessary. You c an

with other pigments c alled speed up the drying process by blowing on the spot

s
accessory pigments. These or using the hairdryer.

e
pigments absorb dierent

10. When the spot is dark enough, slide the other end of

ranges of wavelength of light,

the strip into the slot in a cork or bung that ts into a

r
so they look dierent colours to

tube that is wider than the TLC strip. The slot should

us. Pigments c an be separated

P
hold the strip rmly.

y
by chromatography. You

11. Insert the cork and strip into a specimen tube.

may be familiar with paper

l
The TLC strip should extend nearly to the bottom of
chromatography but thin

n
the tube, without touching it.
layer chromatography gives

better results. This is done

t
12. M ark the outside of the tube just below the level of

O
with a plastic strip that has
the spot on theTLC strip.
▴ Figure 7 Thin layer

i
been coated with a thin layer

chromatography (TLC)

s
13. Take the strip and cork out of the tube.
of a porous material. A spot

containing pigments extracted from leaf tissue is placed

14. In a well-ventilated room (or in a fume cupboard),

y
near one end of the strip. A solvent is allowed to run up
pour running solvent into the specimen tube up to
e
the strip, to separate the dierent types of pigment. (At
the level that you marked.

p
the end of the procedure, methods used for disposal of

15. Place the specimen tube on a lab bench where it

v

solvents must comply with regulations.)

will not be disturbed. C arefully lower the TLC strip

o
i

1. Tear up a leaf into small pieces and put them in and cork into the tube, so the tube is sealed and the

amortar. TLC strip is just dipping into the running solvent. The
n

solvent must NOT touch the pigmentspot.

2. Add a small amount of sand for grinding.

U

16. Leave the tube alone for about ve minutes, to allow

3. Add a small volume of propanone (acetone).

the solvent to run up through the TLC strip. You c an

n

4. Use the pestle to grind the leaf tissue and dissolve out
watch the pigments separate but DO NOT TOUCH

the pigments.
THE TUBE.
o
d

5. If all the propanone evaporates, add a little more.

17. When the solvent has nearly reached the top of the

strip, remove the strip from the tube and separate it

i
r

6. When the propanone has turned dark green, allow

fromthe cork.
t

the sand and other solids to settle. Then pour o the

o

propanone into a watch glass.

18. Rule two pencil lines across the strip, one at the level
a

reached by the solvent and one at the level of the

7. Use a hairdryer to evaporate o the propanone and
f

initialpigment spot.
the water from the cells’ cytoplasm.
x

19. Draw a circle around each of the separated pigment

8. When you have just a smear of dry pigments in the
l

spots. Then mark a cross in the centre of each circle.

O

watch glass, add 3–4 drops of propanone and use a

a

paint brush to dissolve thepigments.

20. Use a ruler with millimetre markings to measure the

distance moved by the running solvent (the distance

v

9. Use the paint brush to transfer a very small amount of

between the two lines) and the distance moved by

the pigment solution to the TLC strip. Your aim is to

each pigment (the distance between the lower line

E

make a very small spot of pigment in the middle of the

and the cross in the centre of thecircle).

strip, 10 millimetres from one end. This spot should

be very dark. To achieve this, put a small drop onto

387
 Interaction and interdependence

Distance
Pigment Colour of pigment R Spot Name of
f

Colour R
f

moved / mm
number pigment
C arotene orange 0.98

1
Chlorophyll a blue green 0.59

s
Chlorophyll b yellow green 0.42

3
Phaeophytin olive green 0.81

s
4
Xanthophyll 1 yellow 0.28

e
5
Xanthophyll 2 yellow 0.15

r
▴ Table 1 Table of standard R
f
values

y
21. C alculate the R value for each pigment, 8
f

usingtheequation:

l
▴ Table 2

y
distance run moved by pigment

n
R =
f

distance runmoved by solvent

t
22. Show all your results in a copy of Table 2, starting

O
i
with the pigment that moved least far.

s
▴ Figure 8 A chromatogram of leaf pigments

y
e

p
Data-based questions: Determining R values for photosynthetic pigments
f
v

o
1. Use the data in Table 1 to sketch a coloured chromatogram. Include the loc ation of the solvent
i

front and the origin in your diagram. [5]

n

2. Thin layer chromatography was used to separate photosynthetic pigments from three eukaryotic organisms:

spinach (Spinacia

Spinacia oleracea Porphyra Fucus

U

oleracea), a red alga

(Porphyra) and a brown

n

β-carotene β-carotene β-carotene

alga (Fucus). Figure

9 shows diagrams
o
d

of the resulting
chlorophyll a

chromatograms.
chlorophyll a
i
r

chlorophyll a

a. Identify two
t

chlorophyll b
o

xanthophyll
pigments that are
a

xanthophylls
found in all three

fucoxanthin
f

organisms. [2]
u
x

b. Deduce the reason chlorophyll c

origin origin origin

for the brown
l
O

appearance of
a

fronds of Fucus. [1]

▴ Figure 9

c. Porphyra also
v

contains phycoerythrin, which is a red pigment.

E

i. Suggest why phycoerythrin is absent from the Porphyra chromatogram. [1]

ii. Predict one colour of light that will be absorbed eciently by phycoerythrin. [1]

388
 Molecules

C1.3.5 Absorption of specic wavelengths of

light by photosynthetic pigments

The rst stage in photosynthesis is the absorption of sunlight. This involves

chemic al substances c alled pigments. Pigments absorb light and so appear

s
dierent colours to us: the colours we see depend on the wavelengths (colours)

s
of light the pigment absorbs and transmits.

e
• White and transparent substances are not pigments. White substances

reflect all wavelengths of visible light, while transparent substances allow all

r
wavelengths to pass through.

• Pigments that absorb all wavelengths of light appear black. (These pigments

y
transform the light energy into other forms of energy, mostly heat.)
▴ Figure 10 Gentian owers contain the

pigment delphinidin, which reects blue

l
• Other pigments absorb some wavelengths of visible light but not others.

light and absorbs all other wavelengths.

n
Forexample, the pigment in a gentian flower absorbs all colours except blue.

The surrounding leaves absorb red and blue

The flower appears blue to us, bec ause this part of the sunlight is reflected

light, so they appeargreen

t
and c an pass into our eye, to be detected by cells in the retina.

O
i
4
A photon is a particle or unit of light. Photons are discrete quantities of energy. Key

s
3

The energy of a photon is related to its wavelength: the longer the wavelength, 16 µg cm
3.5

UA / ecnabrosba
r
32 µg cm
the less energy a photon holds. Photons are absorbed by pigment molecules

y
3
3
64 µg cm
if the energy they hold c auses an electron in an atom of the pigment molecule
e
3

2.5 128 µg cm

to jump to a higher energy level (excitation). A specic amount of energy

p
2
is required for this to happen and this energy is only supplied by certain
v

wavelengths of light.
1.5

o
i

1
P h o t o sy n t h e s i s i nvo l ve s a ra n g e of pi gm e n ts but the main ph o to sy n t h e ti c
n

pi g me n t s a re c h l o ro p hy l l s . All fo r ms of c h l o ro p hy l l a pp e a r a shade of gre e n 0.5

to us. Th i s is be c a u s e p h o to n s in the re d and blue pa r t s of th e s p e c tr u m c an

0
U

exc i te an e l e c tro n in c h l o ro p hy l l , but w ave l e n g th s in the g re e n pa r t s of the 400 450 500 550 600 650 700

s pe c tr u m (b e t w e e n re d and b l u e) c annot. Th e re fo re, mo s t gre e n l i gh t is wavelength / nm

n

re f l e c t e d . Th i s is w hy gre e n is th e do mi n a n t colour in e c o sys t e m s do mi n a te d

▴ Figure 11 Absorption spectra for

by plants.
o
d

pigments extracted from mulberry fruits at

concentrations from 16 to 128 µg of pigment

The wavelengths of light absorbed by a pigment are shown on a graph c alled an
i

per cubic centimetre of solvent. The spectra

r

absorption spectrum.

use arbitrary units (AU) for absorbance,

t

• The horizontal x-axis shows wavelength of light, in nanometres. The sc ale

o

which show relative amounts of light

extends from 400 to 700 nanometres, reflecting the range of wavelengths in

a

absorption at the dierent wavelengths

visible light. It is helpful to show the colours as well.

rather than percentage or absorbance
f

measured with SI units

• The y-axis shows absorption, often as a percentage.
x

Source: Qin C., Li Y., Niu W., D ing Y., Zhang R.,

Shang X. (2010) Czech J. Food Sci., 28: 117-126.

l
O

C1.3.6 Similarities and dierences of

v

absorption and action spectra

An absorption spectrum (Figure 13) is a graph showing the percentage of light

E

absorbed at each wavelength by a pigment or a group of pigments.

An action spectrum (Figure 14) is a graph showing the rate of photosynthesis at

each wavelength of light.

▴ Figure 12 Ripe mulberry fruits (Morus nigra)

389
 Interaction and interdependence

s
s
e
r
P

y
l
y

n
100 chlorophyll a

100
% / n o i tp r o sb a

chlorophyll b

t
sisehtnysotohp

etar

O
carotenoids

i
x am

s
fo

y
% /

e
400 500 600 700

p
wavelength / nm
v

400 500 600 700

▴ Figure 13 Absorption spectra of plant pigments

o wavelength / nm
i
n

▴ Figure 14 Action spectrum for a plant pigment

U

n
o
d

i
r

C1.3.7 Experimental techniques: Techniques for varying concentrations of

o

c arbon dioxide, light intensity or temperature experimentally to investigate the

f

eects of limiting factors on the rate of photosynthesis

x

Part 1: Varying c arbon dioxide concentration has. In the method below, carbon dioxide concentration is
l
O

the independent variable.

If a stem of pondweed such as Elodea, Cabomba or
a

Myriophyllum is placed upside down in water and the

a. Boil enough water to ll a large beaker, then allow

end of the stem is cut, bubbles of gas may be seen to

v

it to cool. This removes c arbon dioxide and other

escape. If these bubbles are collected and tested, they are

dissolved gases.
E

found to be mostly oxygen, produced by photosynthesis.

b. Repeatedly pour the water from one beaker to

The rate of oxygen production can be measured by

another, to oxygenate it. Very little c arbon dioxide will

counting the bubbles. Factors that might aect the rate of

dissolve.
photosynthesis can be varied to nd out what eect this

390
 Molecules

• Keeping the water at 25°C and brightly

illuminating it.

• Repeating bubble counts until several consistent

counts have been obtained.

s
sodium
2. What other factors could be investigated using

s
hydrogen
bubble counts with pondweed? How would you

c arbonate
design each experiment?

e
3. How could you measure the rate of oxygen

r
production more accurately?

P
Part 2: Varying light intensity

y
Photosynthesis rates can be measured in leaf discs, cut out
pondweed

l
of young healthy leaves using a cork borer or the end of a

n
plastic drinking straw. If the discs are placed in a suitable

environment and prevented from drying out, they will

t
continue to photosynthesize for at least a fewhours.

O
water at 25°C

i
3

a. Remove the barrel from a 10 cm plastic syringe and

s
cover the end of the nozzle with a nger. Then pour

3 −3

10 cm of 0.2 mol mm sodium hydrogen carbonate

y
solution into the barrel of the syringe. This will provide
light source
e
a supply of carbon dioxide.

p
b. Put 10 leaf discs into the sodium hydrogen carbonate
v

o
solution. Then replace the plunger of the syringe.
▴ Figure 15 Apparatus for measuring photosynthesis
i

rates in dierent concentrations of c arbon dioxide

c. Hold the syringe vertically with the nozzle pointing

n

c. Cut the end of a stem of pondweed and place it

upwards. Squeeze all the air out of the syringe, then

upside down in the water. The water contains almost

put a nger over the nozzle and pull on the barrel of the
U

no c arbon dioxide, so no bubbles are expected to

syringe. This will create suction, which will draw air out of

emerge. The temperature of the water should be

the air spaces inside the leaf discs. Stop applying suction
n

about 25°C and the water should be very brightly

and take your nger o the end of the nozzle. Tap the

illuminated. Figure 15 shows suitable apparatus.

syringe so the bubbles of gas rise into the nozzle.
o
d

d. Add enough sodium hydrogen carbonate to the

d. Repeat the previous stage several times, until the

beaker to raise the carbon dioxide concentration by

i

leaf discs become denser than the sodium hydrogen

r

−3

0.01 mol dm . If bubbles emerge, count them for

c arbonate solution and sink to thebottom.
t
o

30 seconds; repeating the counts until two or three

e. Place the syringe in a vertic al position at a measured

a

consistent results are obtained.

distance from a light source. M ake sure the discs are

f

e. Add enough sodium hydrogen carbonate to raise the

fully illuminated. As the discs photosynthesize, they
x

–3

concentration by another 0.01 mol dm . Count the

will produce oxygen. Thiswill c ause them to become

bubbles in the same way.

less dense than the solution, so they rise to the top of
l
O

the syringe. Time how long it takes for each disc to

a

f. Repeat the procedure above until further increases

rise to thesurface.

in carbon dioxide do not aect the rate of bubble

v

production. (Note that, non-native pondweeds should

f. Measure the light intensity using a lux meter.

not be disposed of in ponds or other aquatic habitats

g. Repeat with the syringe at dierent distances from the

E

as they may become invasive.)

light source. The relative light intensity is

2

Questions distance

so a suitable range of distances might be 22 mm,

1. Why are the following procedures necessary?

35 mm, 41 mm, 50 mm and 71 mm. Plot a graph of the

• Boiling and then cooling the water before

results for all the light intensities tested.

theexperiment.

391
 Interaction and interdependence

Part 3: Varying temperature

Temperature can be varied using a water bath, heat blocks or

a fermenter. Photosynthesis rates in algae inside a fermenter

can be measured using a data logger and an oxygen

s
electrode to measure oxygen concentration. Alternatively,

pH can be monitored: as carbon dioxide is absorbed from

s
the water and used in photosynthesis, the pH will increase.

e
r
P

y
l
y

n
pH

t
electrode

O
i
culture

s
of Chlorella

r
algae in

y
▴ Figure 16 Using leaf discs to measure the rate of –3
0.2 mol dm
e
photosynthesis
hydrogen

p
temperature thermostatically
carbonate
v

probe controlled
solution

o magnetic heater
i

stirrer
n

▴ Figure 17 Fermenter used for measuring the rate of

photosynthesis at dierent temperatures by data logging

U

Hypothesis: Choosing relevant variables

o
d

Hypotheses are provisional explanations, which require the resulting dependent variable. The variables dened
i
r

repeated testing. During scientic research, hypotheses in the research question should be the ones that are
t

c an either be based on theories and then tested in an directlymeasured.

o

experiment, or be based on evidence from an experiment

a

Questions

that has been c arriedout already.

In each of the following examples, two dierent variables are
f

You c an set hypotheses for the eects of limiting factors

typed in bold. Identify which is the dependent variable and
x

on photosynthesis before beginning an experiment

which is the independent variable.
l

(based on your understanding of the theory) or using data

1. the c ause and the eect
O

from previous experiments.

a

2. what I change and what I observe

Through experimentation, a researcher may begin to

v

wonder about an observed phenomenon. They might 3. the y-variable on a graph and the x-variable

then develop testable explanations for their observations;

4. the eect of humidity on c arbon dioxide

E

these are new hypotheses.

absorption by leaves

When devising a testable hypothesis, you need to

5. the amount of oxygen produced per hour and the

dene the dependent and independent variables.

number of chloroplasts in a unicellular alga

The dependent variable is the outcome variable. The

independent variable is the c ause variable. You usually set

6. the length of time to solve an order of operations

the level of the independent variable and then measure

maths problem versus gender

392
 Molecules

Data-based questions: Photosynthesis rates in red light

Figure 18 shows the results of an experiment in which E ach photon of light is used to excite an electron (raise it

Chlorella cells were exposed to light of wavelengths from to a higher energy level). C alculate how many times each

s
660 nm (red) up to 700 nm (far red). The rate of oxygen electronproduced by photolysis must be excited

production by photosynthesis was measured and the during the reactions of photosynthesis. [2]

s
yield of oxygen per photon of light was c alculated. This

gives a measure of the eciency of photosynthesis at

e
each wavelength. with supplementary light

r
The experiment was then repeated. This time, at each
without supplementary light

of the wavelengths from 660 to 700 nm, the cells were

y
also exposed to light with a wavelength of 650 nm. 0.15

The overall intensity of light was kept the same as in the

l
rep selucelom
rstexperiment.

n
1. Describe the relationship between wavelength

of light and oxygen yield, when there was no

thgil fo

t
0.10

O
supplementary light. [2]

i
negyxo
2. Describe the eect of the supplementary light. [2]

notohp
s
3. The bars for each data point on the graph show

y
0.05
standard error. Explain how error bars such as these

fo dliey
e
help in drawing conclusions from an experiment. [2]

p
4. The probable maximum yield of oxygen was 0.125
v

molecules per photon of light. C alculate how

many photons are needed to produce one oxygen

o 0
i

660 680 700

molecule in photosynthesis. [2]
n

wavelength / nm

5. Oxygen production by photolysis involves this

reaction: ▴ Figure 18 Photon yield of photosynthesis in

U

dierent light intensities

+
n

4H O → O + 2H O + 4H + 4e
2 2 2
o
d

C1.3.8 C arbon dioxide enrichment

i
r

experiments as a means of predicting future

t
o

rates of photosynthesis and plant growth

a

In high light intensity and warm temperatures, rates of photosynthesis are

f

frequently limited by carbon dioxide concentration. This has been demonstrated

x

in greenhouse experiments: both temperature and light intensity are kept constant
l

at optimal levels while CO concentration is varied (the independent variable).

2
O

Increasing carbon dioxide concentration above current atmospheric levels of about

400 ppm has been found to increase rates of photosynthesis and plant growth.
v

When growing crops such as tomatoes, it is now common practice to raise CO

2

levels in greenhouses above normal atmospheric concentrations on sunny days.

E

The extra c arbon dioxide c an come from boilers that burn natural gas to produce

heat or electricity for the greenhouse. More sustainably, it c an come from

compost-making where plant wastes or animal manures are decomposed by

bacteria and fungi.

Before the start of the Industrial Revolution (in about 1780), the c arbon dioxide

concentration of the atmosphere was about 270 ppm. It is forec ast to rise beyond

393
 Interaction and interdependence

550 ppm during the 21st century. This will have wide-ranging consequences.

One obvious hypothesis is that higher atmospheric CO concentrations will

2

increase rates of photosynthesis and plant growth, as they do in greenhouses.

This could happen with eld crops, tree plantations and natural ecosystems. If this

increases plant biomass, it will help to moderate increases in atmospheric c arbon

s
dioxide. This hypothesis is being tested experimentally.

s
The aim of the experiments is to increase CO concentration, while keeping
2

e
other factors unchanged. These experiments c annot be done in laboratories or

greenhouses, where many factors dier from those in open conditions. Instead,

r
they must be conducted “in the free air ” so they are c alled free air c arbon dioxide

enrichment experiments (FACE).

y
The rst series of FACE experiments investigated plant growth in agricultural

l
crops and young tree plantations. A second series of large-sc ale FACE

y
experiments is being set up in natural or semi-natural forests; the rst of these was

n
in a Euc alyptus forest in Australia and the second was in an oak forest in England.

t
Circles of towers are built and c arbon dioxide is then released from these towers.

O
Concentrations of c arbon dioxide in the air inside these circles are monitored;

i
▴ Figure 19 This greenhouse at Thanet
whenever they drop below 550 ppm, more CO is released on the upwind side.

s
2

E arth in southeast England is dosed with

This is done so that any wind blows the c arbon dioxide into the circle rather than

c arbon dioxide as shown in Table 3. The

r
away from it. E ach experiment also includes control plots, where air is released

y
c arbon dioxide is produced by combined

from the towers rather than c arbon dioxide. The questions being asked in this
e
heat and power engines (CHP) which

p
series of FACE experiments include:

burn natural gas. The heat is used to warm

v

1. Does increased atmospheric CO increase the c arbon storage within a

the greenhouse. Some of the electricity
2

o
generated by the engines provides power mature woodland ecosystem?
i

for lighting and other purposes in the

2. Do mineral nutrients, especially nitrogen or phosphorus, become limiting

greenhouse, but much is sold for use

n

factors on uptake of c arbon?

elsewhere. Yields of tomatoes are increased

signic antly by dosing with CO

2
3. What aspects of biodiversity and ecosystem structure and function alter when
U

the ecosystem is exposed to elevated CO ?

2
n

4. How c an lessons from the global network of second-generation FACE

Light CO
2

experiments be generalized to other woodlands and forests?

intensity / concentration /
o
d

−2

J m ppm

You c an follow the progress of these experiments online by searching for the
i

0 400
r

PhenoC am Network and nding the c ameras for “millha”.

t

100 400
o

200 500
f

300 600
u
x

400 700

500 800
l
O

▴ Table 3
v

▸ Figure 20 This oak wood in England is

E

being used for one of the second-generation

FACE experiments. Six circles of towers are

visible. In three of them, the concentration of

CO is enriched to 550 ppm while the trees

2

are in leaf. The other three circles are control

plots, with air released from the towers

instead of carbon dioxide

394
 Molecules

Experiments: Controlled experiments versus controlled variables

When designing an experiment, you must nd methods while all other factors are kept constant, any change

to control variables. Two loc ations for biologic al research in enzyme activity must be due to the changes

s
are “in the eld” or “in the lab”. It is easier to control intemperature.

variables in the laboratory but some experiments c an

You need to understand the dierence between control

s
only be done in the eld. Field research relating to natural
experiments and controlled variables:

ecosystems is done in the habitats of organisms, including

e
• A control experiment—or just control—is any object

human communities. It is particularly useful for areas of

or system used as a standard of comparison in an

r
biology such as behavioural ecology or epidemiology.
experiment. A control is prepared or c arried out

Laboratory research is used for areas such as biochemistry,

exactly as the other parts of an experiment, except

y
molecular biology, cell biology and physiology. It can
for one variable which is dierent. This allows the

involve whole organisms that have been taken out of their

investigator to assess the signic ance of that variable.

l
natural habitats. More commonly, it involves material such
For example, in an enzyme experiment, a control

n
as biological molecules, organelles, cells, tissues or organs.
experiment might use an enzyme that has been

There are two broad approaches to research in science: denatured by boiling, rather than an active (unboiled)

O
observations and experiments. enzyme, to show that enzyme c atalysis is involved.

i
• Structured observations are particularly suited • A controlled variable is any factor that could vary but

s
to ecology, where the aim is to investigate what is kept at the same level in all parts of the experiment,

r
happens in natural ecosystems without any human so it does not inuence the results of the experiment.

y
intervention. They are also commonly used with For example, in an experiment to investigate the
e
aspects of human biology where experimentation eect of temperature, substrate concentration and

p
is problematic or unethic al. A potential weakness pH would be controlled variables. Any experiment in
v

of research based on observation is that multiple which all variables except the independent variable

factors may aect a variable, so correlations between are c arefully

ocontrolled is c alled a fair test.

i

variables do not show that there is a c ausal link.

Generally, research in labs is experimental and research in
n

• Experiments form the basis of much biologic al the eld is oen based on observations. However, this is

research. The main benet of experiments with not an absolute rule. Biologists sometimes plan research
U

eective control of variables is that it is possible to that combines the benets of experiments and eld
n

be sure about c ausation. For example, in an enzyme conditions, such as the FACE experiments described in

experiment where temperature is deliberately varied Section C1.3.8

o
d

LHA
C1.3.9 Photosystems as arrays of pigment
i
r

molecules that c an generate and emit

o

excitedelectrons
f

Photosystems are pigment–protein complexes located in the thylakoid membranes

u
x

of chloroplasts. In a typical photosystem, there are about 100chlorophyll molecules

and 30 accessory pigment molecules arranged in a precise molecular array;

l
O

however, there is a lot of variation between the photosystems that have evolved in
a

dierent organisms. Carotene and xanthophyll are examples of accessory pigments.

v

E ach photosystem has a core complex, connected to light-harvesting antenna

complexes. Pigment molecules within antenna complexes absorb light bec ause
E

it c auses an electron in one atom of the pigment to become excited and jump

to a higher energy level. A specic amount of energy is required for this to

happen; this precise amount of energy is only supplied by certain wavelengths.

The amount of energy decreases as the wavelength increases so, for example,

photons of blue light have more energy than photons of red light.

The light energy that is absorbed by a pigment can be re-emitted as light when the

electron drops back down to its original energy level. This is called uorescence.

395
 Interaction and interdependence
LHA

However, something dierent happens in a light-

harvesting complex. When the excited electron in a

pigment molecule drops back down to its original

level, the energy emitted is absorbed by an electron in

the adjacent pigment molecule, causing it to become

s
excited. This process is called excitation energy transfer

and it is repeated across the light-harvesting complex. In

s
this way, energy is transferred from pigment to pigment

e
until it reaches the reaction centre in the core complex.

This process happens very rapidly, taking only a few

r
▴ Figure 21 This image of photosystem femtoseconds. For this energy transfer to happen, the pigment molecules must be

II is from the PDB-101 website; on this site,

held in a precise array, in terms of both the distances between them and their relative

y
you c an rotate the image to study the details
orientations. This is achieved by the protein subunits in the light-harvesting complex.

of the structure. Chlorophyll molecules

l
are shown bright green and accessory Light energy absorbed by any of the pigments in the light-harvesting complex

n
pigments such as c arotene are pink. Protein
is funnelled into the core complex. Eventually, it reaches a special pair of

chains in the dierent antenna complexes

chlorophyll molecules in the reaction centre. These molecules are able to donate

t
within the light-harvesting complex are
pairs of excited electrons to electron acceptors. This completes the task of the

O
shown in yellow and blue. In the core

i
photosystem. Light energy has been absorbed, generating excited electrons.

complex they are dark green

s
These electrons are then emitted from the photosystem, c arrying the energy

needed for later stages of photosynthesis.

y
In low light intensities, this process is very ecient—more than 99% of
e

p
photons that are absorbed result in excited electrons being emitted from the

photosystem. In high light intensities, other factors make harvesting less ecient
v

and some of the light energy absorbed is re-emitted by uorescence.

o
i

There are two types of photosystem in the chloroplast of a plant, with dierent
n

functions. The dierences between them are shown in Table 4.

Photosystem I Photosystem II
U

Loc ation in the chloroplast Mostly loc ated in thylakoid membranes Mostly located in thylakoid membranes in
n

between grana, c alled stroma lamellae grana, which are cylindrical stacks ofthylakoids

Primary electron donor in P700, containing a pair of chlorophyll P680, containing a pair of chlorophyll
o
d

the reaction centre molecules with peak light absorbance at molecules with peak light absorbance at

700 nm 680 nm
i
r

Transfer of excited To the enzyme NADP reductase, which uses To plastoquinone which transfers the
t
o

electrons from the primary the electrons to reduceNADP electrons on to a chain of electronc arriers
a

electron donor
f

Source of replacement Two electrons from plastocyanin Photolysis of water

u
x

electrons
l
O

▴ Table 4
a

C1.3.10 Advantages of the structured array

v

of dierent types of pigment molecules in

aphotosystem
E

There are signic ant advantages in having pigment molecules arranged in the

structured array of a photosystem:

• Photons of light are sc attered. Even in high-intensity light, one pigment

molecule would only intercept a few photons per second. A photosystem

combines over 100 pigment molecules, increasing the number of photons

absorbed per second by two orders of magnitude.

396
 Molecules

LHA
• Individual pigment molecules only absorb light in a narrow range of

wavelengths. The range varies between pigments. For example, chlorophylls

do not absorb green wavelengths but c arotene does. A photosystem

combines different types of pigment in one array, so a greater proportion of

the energy in sunlight c an be used.

s
• Energy is only transferred from one pigment molecule to another when the

s
molecules are in a close and precise orientation. Otherwise, light energy is

lost by fluorescence. The structured array also ensures that absorbed energy

e
is funnelled to the reaction centre of the photosystem.

r
The pigment molecules in the structured array of a photosystem are

P
interdependent. Individually they could not perform any part of photosynthesis;

y
together, they c an harvest light energy very eciently, allowing photosynthesis.

l
The functioning of photosystems is increasingly understood but there are still

n
many unanswered questions. The mechanisms used do not involve molecular

motion or enzyme–substrate collisions. The interactions that occur within

O
photosystems are complex and c an only be explained using the principles of

i
quantum mechanics. This is therefore a biologic al topic that has become the

s
domain of biophysicists rather than biochemists.

y
e

p
Data-based questions: Photosynthesis in articial light
v

The light-source spectra in Figure 22 show

relative amounts of light of dierent wavelengths

o
i

in sunlight and in articial sources of light such as

n

LED lamps.

1. Compare and contrast the spectra for daylight

U

at noon and for white LED lamps. [2]

n

2. The action spectrum for photosynthesis,

Figure 14 on page 390, shows that

o
d

photosynthesis happens most rapidly in

blue or red light. A combination of red

i
r

and blue light usually gives higher rates

t

of photosynthesis than red or blue light

o

only. Suggest reasons for low levels of

a

photosynthesis at sunset. [2]

f

3. White LED lamps are used to illuminate homes

x

and other places where humans need articial

l

light. Discuss whether cool white LED lamps

O

or warm white LED lamps are more suitable for

homes in the evening. [2]

v

4. LEDs are widely used as articial light sources

for crops grown in articial conditions.

E

Suggest reasons for using a combination of

▴ Figure 22

red and blue LEDs, rather than white LEDs, for

photosynthesizing plants. [2]

5. Blue light promotes the opening of stomata. Explain how rates of photosynthesis might be restricted in plants grown

in light only from red LEDs. [4]

397
 Interaction and interdependence
LHA

Activity: Leaf colours

Suggest a hypothesis for most naturally occurring plants

not having black leaves (that is, explain why plant leaves

s
do not absorb all the colours of light).

s
e
r
P

y
l
y

n
t

O
i
s
r

y
e
▴ Figure 23 Growing leaves on Viburnum tinus are orange-

p
▴ Figure 24 There are a few garden plants with very dark
red and then turn green. M any trees produce leaves that are
v

leaves, but they are selected varieties that would not thrive
red while they are young and growing, but green when they

o
in natural ecosystems. The plant shown is the “Black Sc allop”
are mature. C an you suggest a hypothesis for this? C an you
i

variety of the decorative plant Ajuga reptans

nd any loc al plants with leaves that are ush red at rst? Why
n

do leaves not ush blue?

U

C1.3.11 Generation of oxygen by the

photolysis of water in photosystem II

o
d

Absorption of photons of light by photosystem II c auses a special chlorophyll

(P680) in the reaction centre to become oxidized by emitting excited electrons.

i
r

P680 is a powerful reducing agent, which is able to regain electrons from water.
t
o

This happens in the oxygen-evolving complex (OEC) of photosystem II. The OEC
a

contains a group of manganese, c alcium and oxygen atoms and is in the core
f

complex of the photosystem, next to the thylakoid space.

u
x

The OEC binds two water molecules and splits them to release four electrons and

four protons. The remaining two oxygens bond together to produce a molecule
l
O

of oxygen (O ).
a

2H O → O + 4H + 4e
2 2
v

This splitting of water is c alled photolysis bec ause it only happens in the light,
E

when the P680 chlorophyll is oxidized.

Photolysis happens in the OEC on the inner surface of thylakoid membranes. The

electrons are transferred to the reaction centre, to replace those emitted by the

P680 chlorophyll. The protons are released into the thylakoid space, contributing

to a proton gradient across the thylakoid membrane. Oxygen molecules

produced by photolysis are a waste product. They diuse out from the thylakoids

to the stroma of the chloroplasts. From there, they diuse through the cytoplasm

398
 Molecules

LHA
of the cell and eventually out of the organism. In plants with

leaves, the oxygen diuses out through the stomata.

For hundreds of millions of years, the E arth’s atmosphere

contained little or no oxygen, so elements such as iron existed

s
mostly in a reduced state. The production of oxygen by photolysis

in cyanobacteria led to the oxidation of iron and other elements.

s
For example, 2,500 to 2,800 million years ago, iron dissolved

e
in the oceans was oxidized to iron oxide and precipitated. This

led to the formation of sedimentary rocks known as banded iron

r
formations.

P
Once iron and other elements had been oxidized, oxygen

y
started to accumulate in the atmosphere. This allowed aerobic ▴ Figure 25 The increase in oxygen concentrations in the

oceans between 2,800 and 2,500 million years ago c aused

l
respiration to evolve in bacteria. L ater in the history of the E arth,

y
dissolved iron in the water to oxidize to insoluble iron oxide,
chloroplasts evolved by endosymbiosis from cyanobacteria.

n
which precipitated on the sea bed. This led to the formation
Eukaryotic algae and then plants also began to contribute oxygen

t
of distinctive banded iron formations, with layers of bright

to the atmosphere, so concentrations continued to rise.

O
red iron oxide alternating with other minerals

i
s
Data-based questions: Changes in atmospheric oxygen

y
e
40

p
erehpsomta

o
30
i
n

C
fo

20
% / negyxo

10
o
d

3.0 2.0 1.0 0

i
r

millions of years ago (×1,000)

t
o

▴ Figure 26 Changes in atmospheric oxygen concentration over time

f

1. Use the graph in Figure 26 to describe the changes 5. Suggest the c auses for these dierences
x

in atmospheric oxygen concentration over the between the planets. [3]

l

history of the E arth. [3]

O

Planet Composition of atmosphere / %

a

2. Determine the highest level of atmospheric

CO N Ar O H O
oxygen and the time when it occurred. [2] 2 2 2 2
v

Venus 98 1 1 0 0

3. Research and suggest an explanation for

E

these changes. [4] E arth 0.04 78 1 21 0.1

M ars 96 2.5 1.5 2.5 0.1

4. Look at the data in Table 5. Compare the composition

of the E arth’s atmosphere with that of Venus and

▴ Table 5

M ars. Include only the largest dierences in your

answer. [3]

399
 Interaction and interdependence
LHA

s
s
e
O OH

r
H C H C
3 3

y
+

+ 2e + 2H

H C H H C H
3 3

l
y

n
O CH OH CH
3 3

9 9

t
plastoquinone plastoquinol

O
i
s
r

y
e

p
v

o
i
n

C
U

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

400
 Molecules

p
p

LHA
+

h
h
2H

o
o
NADP proton pumping

t
o

o
il
l

n
i

n
and NADP reduction

g
g

2H

s
h
h

reduced

o
t
t

remove protons

f
NADP

from the stroma

2e

s
PSII PSI
2e
2e
proton pumping and photolysis add

s
protons to the thylaoid space lumen

The volume of this space is very small so a

e
+ + +
2H O
2 4H 2H H
high proton concentration is achieved y

pumping relatively small numers of protons

r
ATP synthase uses

P
ADP

y
the proton gradient

O
2
ATP
to produce ATP

l
y

n
▴ Figure 27 Production of ATP is based on interaction between components ofthylakoids

O
i
Data-based questions: Evidence for chemiosmosis

s
One of the rst experiments to give evidence for ATP

r
3

y
production by chemiosmosis was performed in the

md
summer of 1966 by André Jagendorf. Thylakoids were
e
3.8

lomµ / noitcudorp

p
incubated for several hours in darkness, in acids with a pH
v

ranging from 3.8 to 5.2. The lower the pH of an acid, the

o
higher its concentration of protons. During the incubation,
i

protons diused into the space inside the thylakoids,

until the concentrations inside and outside were equal.

n

The thylakoids were then transferred, still in darkness, 4.8

PT A

into a solution of ADP and phosphate that was more

U

5.2

alkaline. There was a brief burst of ATP production by the

n

thylakoids. Thegraph shows the yield of ATP at three acid

6.5 7.0 7.5 8.0 8.5

incubation pHs and a range of pHs of the ADP solution.

pH of ADP solution
o
d

1. a. Describe the relationship between pH of

ADP solution and ATP yield, when acid incubation ▴ Figure 28 Results of the Jagendorf experiment
i
r

was at pH 3.8. [2]

t

3. Explain why there was only a short burst of

o

b. Explain why the pH of the ADP solution

ATP production. [2]

a

aects the ATP yield. [2]

4. Explain the reason for performing the

f

2. Explain the eect of changing the pH of acid

u

experiment in darkness. [2]

x

incubation on the yield of ATP. [2]

l
O

C1.3.13 Reduction of NADP by photosystem I

v

Production of c arbon compounds (such as glucose) by photosynthesis requires a

supply of electrons. This is provided by NADP (nicotinamide adenine dinucleotide

E

phosphate). NADP is identic al to NAD, which is used in cell respiration, except that it

has one extra phosphate group. Like NAD, NADP c an exist in either a reduced or an

oxidized state. It is converted to the reduced state by accepting two electrons:

NADP + 2e → reduced NADP

401
 Interaction and interdependence
LHA

Reduced NADP is produced by photosystem I. Energy from photons of light is

absorbed by pigment molecules in the photosystem and passed to the reaction

adenine

centre. Here, it reaches a special pair of chlorophyll molecules (P700) that act as

the primary electron donor. An electron in one of these chlorophyll molecules is

excited and then emitted from the reaction centre. It is passed via a short chain of

s
electron c arriers to the enzyme NADP reductase. This enzyme is positioned on

the stroma side of the thylakoid membrane where it c an receive electrons from

s
photosystem I. When NADP reductase has received two excited electrons, it c an

e
convert a molecule of NADP in the stroma to reduced NADP.

r
nicotinamide Electrons from photosystem I that are used to reduce NADP are replaced by

electrons c arried by plastocyanin. Photosystems I and II are therefore linked:

y
electrons excited in photosystem II are passed via plastoquinone and cytochrome

b f to plastocyanin, which transfers them to photosystem I.

6

l
y
The supply of NADP in a chloroplast sometimes runs out, bec ause it has all

n
▴ Figure 29 In this diagram of NADP, been converted to reduced NADP. When this happens, excited electrons from

t
ribose is shown as a blue pentagon and
photosystem I are diverted to plastoquinone instead of being passed to NADP.

O
phosphate as a violet circle. The structure
As the electrons ow back to photosystem I via cytochrome b f and plastocyanin,

i
6

of NAD is the same, without the extra

they c ause proton pumping which allows ATP production by chemiosmosis.

s
phosphate on the nicotinamidenucleotide

This process is cyclic photophosphorylation. It allows ATP to be produced when

r
production of reduced NADP is impossible or unnecessary.

y
e

p
v

C1.3.14 Thylakoids as systems for

performing the light-dependent reactions o

i
n

of photosynthesis

A thylakoid is a sac-like vesicle that performs the light-dependent reactions of

U

photosynthesis. In these reactions, light energy is absorbed and used to split

n

water by photolysis, reduce NADP and produce ATP by chemiosmosis.

Cyanobacteria have thylakoids that are variable in shape and are attached to the
o
d

plasma membrane. Eukaryotic algae and plants have two types of thylakoid inside

their chloroplasts:
i
r

• disc-shaped thylakoids are arranged in stacks c alled grana

t
o

• unstacked thylakoids, known as stroma lamellae, form connections between

a

thylakoids in grana.
f

u
x

one thylakoid
l
O

a
v
E

granum — a stack
▸ Figure 30 An electron micrograph of a

of thylakoids
pea chloroplast

402
 Molecules

LHA
thylakoid

s
s
stroma

lamellae

e
r
granum — a stack

y
of thylakoids

l
Figure 31 Stroma lamellae are

y
surrounded by stroma whereas most

n
thylakoids in the grana have minimal contact

t
with the stroma. Photosystem 1 arrays and

O
ATP synthases are mostly in the stroma

i
lamellae and photosystem II arrays and

s
cytochrome B f complexes are mostly in
6

the grana. C an you suggest reasons for this

y
e distribution of components?

p
v

o
i
n

oxygen
U

n
o
d

ADP ATP

+
2H
i
r

PSII

ey
t

2e OEC ATP
o

PSI hotosysteI
synthase
a

H O
2
PSII hotosysteII +
2H
f

PQ
u

PQ lastouinone
x

+
PQH  lastouinol
2
2H
l

PC lastocyanin
O

+
PQH +
2 2H
2H
a

NRase NADPreductase PSI

2e
NRase
NADP
PC PC

OEC oxygeneoling
e
v

cyt  2e
colex  reduced

NADP
E

cyt  cytochroe 
 

thylakoid thylakoid stroa

sace erane

▴ Figure 32 This diagram shows part of one thylakoid and how the four main complexes

within it interact through transfers of protons and electrons to produce ATP and reducedNADP

403
 Interaction and interdependence
LHA

HO OH

OH

s
glyceric acid

s
O

e
P O OH

r
OH

y
3-phosphoglyceric acid

l
O

n
t
P O O

O
i
OH

s
glycerate 3-phosphate

r
Rubisco

y
▴ Figure 33 What are the dierences

between the three substances shown here?

e

p
What are the similarities between glyceric

acid and glycerol (see Figure 20 on page

v

188; Section B1.1.9)?

o
Rubisco is surprisingly inecient. Most enzymes convert thousands of molecules
i

of substrate to product per second. However, Rubisco only xes about three CO
2

molecules per second. To compensate for this, there are very high concentrations
n

of Rubisco in the stroma. It is thought to be the most abundant enzyme: the total

mass on E arth was recently estimated to be 0.7 Gt (700billion kilograms).

U

C1.3.16 Synthesis of triose phosphate using

o
d

reduced NADP and ATP

i
r

In sugars and other c arbohydrates, there are twice as many hydrogen atoms as
t

oxygen atoms. RuBP is a ve-c arbon sugar derivative. It is converted to glycerate

o

3-phosphate by the addition of c arbon and oxygen, but not hydrogen; as a

result, the amount of hydrogen relative to oxygen becomes less than two to one.
f

O Hydrogen has to be added to glycerate 3-phosphate by a reduction reaction to

x

produce c arbohydrate. The c arboxyl group in glycerate 3-phosphate is replaced

C
l

by an aldehyde group.
O

OH

This conversion involves both ATP and reduced NADP, produced by the light-

carboxyl group
dependent reactions of photosynthesis. ATP provides the energy needed to
v

perform the reduction and reduced NADP provides the electrons (contained

in hydrogen atoms). The product is a three-c arbon sugar derivative, triose

E

phosphate. Oxygen removed from the c arboxyl group combines with hydrogen

C H
from reduced NADP to produce water.

aldehyde group

Conversion of glycerate 3-phosphate to triose phosphate happens in the stroma

▴ Figure 34 C arboxyl and aldehyde of the chloroplast. It is part of the light-independent reactions of photosynthesis

groups bec ause light is not directly used. However, it c an only continue for a short time

in darkness as ATP and reduced NADP are required and they quickly run out.

404
 Molecules

LHA
C1.3.17 Regeneration of RuBP in the C alvin

ribulose

cycle using ATP

bisphosphate

The rst c arbohydrate produced by the light-independent reactions of

photosynthesis is triose phosphate. Two triose phosphate molecules c an be CO

s
2

combined to form hexose phosphate. Hexose phosphate molecules c an be

s
Rubisco
combined by condensation reactions to form starch. When conditions in a leaf

are suitable for photosynthesis, starch rapidly accumulates in chloroplasts.

e
2 glycerate

If all of the triose phosphate produced by photosynthesis was converted to

r
3-phosphate

hexose or starch, the supplies of RuBP in the chloroplast would soon be used up.

P
This would c ause c arbon xation to stop. Therefore, some triose phosphate has

y
2ATP

to be used to regenerate RuBP. This process is a conversion of a three-c arbon

sugar into a ve-c arbon sugar and it c annot be done in a single step. Instead a
2ADP +

l
series of reactions take place.

y
2 phosphates

n
The light-independent reactions of photosynthesis form a cycle, in which RuBP is

O
both consumed and produced. This cycle was named the C alvin cycle to honour
2 reduced NADP

i
Melvin C alvin, who was given the Nobel Prize in Chemistry in 1961 for his work in

s
elucidating this process. 2 NADP

r
For the Calvin cycle to continue indenitely, as much RuBP must be produced as

y
2 triose phosphate

consumed. When RuBP and CO are combined by Rubisco, only one of the six
e
2

p
carbon atoms is newly xed. For this reason, only one-sixth of the triose phosphate

molecules that are produced can be taken out of the Calvin cycle. Five-sixths of the
v

▴ Figure 35 Summary of c arbon xation

triose phosphate must be used to regenerate RuBP. For a net gain of one molecule

o
reactions
i

of hexose, the Calvin cycle must happen six times to x six carbon atoms.
n

Regeneration of RuBP requires the use of ATP. This is bec ause triose phosphate is

converted into ribulose phosphate and this must be converted to RuBP.

U

5 triose

phosphate
o
d

3(ADP + phosphates)

ribulose
3 CO

i
r

bisphosphate
3ATP
t

Rubisco
o

 lycerate
f

3 ribulose
u

CALVIN phosphate

bisphosphate
3 ribulose
x

CYCLE

phosphate
l

ATP
O

AT P
a

3ATP

 phosphates

5 triose
3(ADP + phosphates)
v

 reduced ADP

phosphate

 ADP
E

One triose

3 ribulose bisphosphate

phosphate can be

removed from the

▴ Figure 37 Summary of RuBP

cycle

regeneration

▴ Figure 36 The C alvin cycle

405
 Interaction and interdependence
LHA

C1.3.18 Synthesis of c arbohydrates,

amino acids and other c arbon compounds

using the products of the C alvin cycle and

s
mineralnutrients

s
Simple equations for photosynthesis usually show glucose as the end product.

Plants require large quantities of glucose for cell respiration and for making cellulose.

e
Six turns of the Calvin cycle are needed to produce one molecule of glucose; each

r
turn of the cycle contributes one of the xed carbon atoms inglucose.

▴ Figure 38 Two large starch grains c an

P
Glucose is usually converted to sucrose for transport from leaves to other

y
be seen inside this chloroplast, the larger

parts of the plant. At times, glucose is produced more quickly than it c an be

of which is over a micrometre long. There

transported. At these times, it is converted to starch and stored temporarily inside

l
are also some dark spheres which are oils.

y
chloroplasts. At night, when photosynthesis has stopped, this starch is broken

n
Outside the chloroplast, parts of the plasma

down and the c arbohydrate is exported from the leaf.

membrane, cell wall and vacuole of the cell

t
are visible.

O
Chloroplasts c an also convert triose phosphate from the C alvin cycle into fatty

i
acids, using enzymes of the glycolysis pathway and link reaction to produce

s
acetyl coenzyme A and then linking together two-c arbon acetyl groups. Glycerol

c an also be made from triose phosphate and linked to fatty acids to produce

y
triglycerides. Droplets of stored oil are oen visible in chloroplasts.
e

p
M any other c arbon compounds c an be produced in photosynthesizing cells,

starting either with glycerate 3-phosphate or triose phosphate from the C alvin
v

o
cycle or with intermediates from pathways used for aerobic respiration. Mineral
i

nutrients such as phosphate or sulfate are also needed to make compounds

containing elements other than c arbon, hydrogen and oxygen. All 20 amino
n

acids are synthesized in photosynthesizing organisms, using branching metabolic

pathways; nitrogen is supplied by nitrate or ammonium ions.

U

C1.3.19 Interdependence of the light-

o
d

dependent and light-independent reactions

i
r

Light-dependent reactions in the thylakoid Light-independent reactions in the stroma

o

membranes or on the surface of them

f

o photolysis o c arbon fixation

u
x

o light absorption by generation of excited electrons o synthesis of triose phosphate and other c arbon

compounds
l

o transport of electrons by c arriers

O

o regeneration of RuBP

o ATP synthesis by chemiosmosis

v

o reduction of NADP
E

▴ Table 6 Comparison of the two parts of photosynthesis

406
 Molecules

chloroplast

LHA
Despite the name, light-independent reactions

envelope
thylakoid
c an only continue for a few seconds in darkness.

membranes
This is bec ause they are dependent on substances
carbon

produced by the light-dependent reactions,

dioxide
water

which rapidly run out if they are not produced

oxygen

s
continuously. Similarly, light-dependent reactions

s
c annot continue indenitely without substances

produced by the light-independent reactions. The

ATP NADP

e
two parts of photosynthesis are interdependent.
reduced ADP
glucose

NADP

r
Light intensity aects which part of photosynthesis

stroma
limits the overall rate at which c arbon compounds

y
are produced.

• In low light intensity, the production of ATP

▴

l
Figure 39 NADP/reduced NADP and ATP/ADP are exchanged

and reduced NADP are restricted. Therefore,

y
between the two parts of photosynthesis

n
the conversion of glycerate 3-phosphate in the

t
C alvin cycle is the rate-limiting step. 6CO C H O
2 6 12 6

O
i
• In high light intensity, c arbon fixation is usually

the rate-limiting step. Use of reduced NADP is

s
18 ATP 18 ADP + phosphate

restricted, so supplies of NADP limit the light-

12 reduced NADP 12 NADP

y
dependent reaction. Some photons of light

absorbed by the photosystems are re-emitted

e
▴ Figure 40 Three ATP and two reduced NADP molecules

p
as fluorescence.
allow one turn of the C alvin cycle in the stroma. Six times as much
v

reduced ATP and reduced NADP are needed to synthesize one

o
molecule of glucose
i
n

Data-based questions: The eect of light and dark on c arbon dioxide xation

One of the pioneers of photosynthesis research was

U

light dark

James Bassham. The results of one of his experiments are

n

shown in Figure 41. Concentrations of RuBP and glycerate

3-phosphate were monitored in a culture of cells of the

noitartnecnoc
o
d

alga, Scenedesmus. The algae were initially kept in bright

light and then in darkness.

i
r

1. Compare the eects of the dark period on the

t

concentrations of RuBP and glycerate

o

glycerate 3-phosphate
e v it a l e r
a

3-phosphate. [2]
f

2. Explain the change that took place in the 25 seconds

u

ribulose bisphosphate

aer the start of darkness, to the concentration of:

x

a. glycerate 3-phosphate [3]

l
O

b. RuBP. [1]

0 100 200 300 400 500 600 700

3. Predict the eect of turning the light back on aer the
v

time / s
period of darkness. [2]
E

4. Predict the eect of reducing the c arbon dioxide

concentration from 1.0% to 0.003%, instead of

light off

changing from light to darkness:

▴ Figure 41 Results of the Bassham experiment

a. on glycerate 3-phosphate concentration [2]

b. on RuBP concentration. [2]

407
 Interaction and interdependence
LHA

Experimental techniques: Creating and interpreting absorption spectra

To test the light-absorbing properties of plant pigment: and immerse them in isopropyl alcohol in separate tubes.

This will allow you to determine the absorption spectrum

a. isolate the pigment in solution

s
of a single pigment. (You will obtain better results if you

b. place the solution in a glass cuvette

combine your coloured bands with those of several other

s
c. place the cuvette in a spectrophotometer or students in the test tube.)

e
colorimeter
Figure 42 shows the absorption spectra for pigments from

two types ofleaf.

d. pass light of dierent wavelengths through the

r
1. Compare the absorption of the pigment samples
solution, from violet (400 nm) to red (700 nm) and

shown in Figure 42, including similarities and

P
back again

y
dierences. [3]

e. record the values from the detector on the other side

l
2. Deduce, with reasons, which curve shows the
of the cuvette, which will determine the proportion of

y
absorption of the pigments from the Fagus leaf

n
light of each wavelength absorbed by the solution

and which shows the absorption of the pigments

f. plot these values to show the absorption spectrum for

t
from the Acer leaf. [2]

O
the pigment.

i
3. Suggest why plants use pigments that absorb light

To isolate the pigment, grind spinach leaves in an organic

s
in the range 400–700 nm and not higher or lower

solvent such as propanone with some sand for abrasion.

wavelengths. [3]

r
(This must be done in a well-ventilated space.) You c an

y
4. Some algae growing on rocky beaches have a
use this solution to produce an absorption spectrum for
e
brown colour. Predict, with reasons, the absorption

p
the combined pigments of theleaves.

spectrum for the pigments in these algae. [2]

v

Alternatively, c arry out paper chromatography with the

o
spinach leaf extract. Aer separation has occurred, cut out
i

the dierent coloured bands on the chromatogram

n

C
U

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v

▴ Figure 42 Absorption spectra for pigments from two types of leaf: a green leaf of Fagus sylvatica (beech) and a leaf of Acer
E

palmatum ( Japanese maple), which contained a red pigment in addition to chlorophyll

408
 Molecules

LHA
Experimental techniques: Investigating photosynthesis with immobilized algae

Alginate beads containing immobilized unicellular algae • number of beads.

c an easily be prepared.

Possible dependent varaibles include:

s
1. Algae are cultured in a nutrient-rich liquid medium.

• change in pH of uid around the beads

Chlorella, Scenedesmus and some species of

s
• oxygen concentration of uid around the beads
cyanobacteria are suitable.

e
• colour change of a redox or pH indic ator.
2. The algae are concentrated by centrifugation.

3 3

r
3. A mixture of 2 cm of concentrated algae with 8 cm

of 2% sodium alginate solution is made in a 10 cm

y
syringe.

4. The algae–alginate mixture is dripped into 2% c alcium

l
chloride solution, to create spheric al beads, which

n
harden in 5 minutes.

t
5. The beads are then separated and rinsed to remove

O
i
the c alcium chloride solution.

s
M any experiments could be performed using the algal

beads—you may choose.

y
• You should vary one factor aecting photosynthesis.
e
This is the independent variable.

p
v

• You will need a method of measuring the rate of

o
photosynthesis. This is the dependent variable.
i

Possible independent variables include:

n

• light intensity

• light wavelength
U

▴ Figure 43 Alginate–algae beads

n
o
d

Linking questions
i
r

1. What are the consequences of photosynthesis for ecosystems?

t
o

a. Outline the c arbon cycle. (C4.2.17)

a

b. Explain the mechanism of oxygen generation by plants.(C1.3.11)

f

u
x

c. Distinguish between primary production and secondary production

in ecosystems. (C4.2.15)
l
O

2. What are the functions of pigments in living organisms?

a

a. The plumage of a bird of paradise is an adaptation that contributes

v

to mate selection. Use the example of mate selection to describe the

concept of a selection pressure.(D4.1.7)

E

b. Outline the role of colour in pollination. (D3.1.9)

c. Explain how an action spectrum is determined experimentally.

(C1.3.6)

409
 Interaction and interdependence

TOK

C an new knowledge change established

s
s
values or beliefs?

e
Planck (1949, pp. 33–34) states:

r
A new scientic truth does not triumph by convincing In 1961, Peter Mitchell proposed the chemiosmotic

P
its opponents and making them see the light, but rather hypothesis to explain the coupling of electron transport

y
because its opponents eventually die, and a new generation in the inner mitochondrial membrane to ATP synthesis.

grows up that is familiar with it. Thishypothesis was a radic al departure from the dominant

l
y
paradigm and was not generally accepted for many years.

n
In 1962, the physicist Thomas Kuhn published a book

Mitchell was awarded the Nobel Prize in Chemistry in

called The Structure of Scientic Revolutions. In it, he argued

t
1978. In his Nobel Prize speech, Mitchell stated that art

O
for a revision in our understanding of how science makes

and science share something in common in that they oen

i
progress. At that time, K arl Popper had been one of the most

involve an “imaginative jumping forward” followed by a

s
inuential writers on the philosophy of science. According

critic al view on what has gone before. His own experience

to Popper, science is based on objective eorts to refute

r
of this phenomenon led him to c aution that the imaginative

y
rather than conrm theories. Science makes progress by

leap forward is a hazardous activity:

e
falsication—by establishing with certainty what is not true.

p
“In the experimental sciences, the scientic fraternity
v

must test a new theory to destruction, if possible.

o
Meanwhile, the originator of a theory may have a very
i

lonely time, especially if his colleagues nd his views of

n

nature unfamiliar, and dicult to appreciate.”

U

n
o
d

i
r

t
o

a
f

▴ Figure 2 Peter Mitchell and Jennifer Moyle. Moyle designed

x

many of the experiments that were fundamental in testing the theory

l

of chemiosmosis
▴ Figure 1 The front cover of the rst edition
O

of The Structure of Scientic Revolutions

A framework for interpreting observations such as a theory

v

is known as a paradigm. Kuhn suggested that scientists

are oen deeply embedded in an existing paradigm. As a

E

result, they may be reluctant to refute the theories around

which they have built their c areers. Instead, many scientists

commit themselves to a paradigm even when mounting

evidence c annot be explained by it.

410
 Molecules

End of chapter questions

stinu
1.2
1. The rate of c arbon dioxide uptake by the green succulent

1.1

yrartibra / noitcaer
shrub Aeonium goochiae c an indic ate the amount of
1.0
Source: Taber,

s
0.9
photosynthesis taking place in the plant. This rate was
R.L. (1998), The

0.8

competitive inhibition
measured at 15°C and 30°C over a 24-hour period.
0.7

s
of yeast alcohol
−1 0.6

The units of c arbon dioxide absorption are mg CO h .

2
0.5 dehydrogenase by

e
The results are shown below. The centre of the graph

fo
0.4
2,2,2-triuoroethanol.

et a r
0.3 no inhibition
−1

Biochem. Educ., 26:

corresponds to −2 mg CO h and the outer ring is
3
2 1 mmol dm inhibitor
0.2

r
l a it i n i
−1 239-242. https://doi.
3
+2.5 mg CO h 0.1 3 mmol dm inhibitor

org/10.1016/S0307-
0

Key

P
4412(98)00073-9
0 10 20 30 40 50 60 70 80 90 100

y
30°C
3
ethanol concentration / mmol dm
2400 (midnight)
15°C

2.5
2300 0100

l
2 0200
a. Outline the effect of increasing the substrate
2200

1.5

y
0300 (early morning)

n
2100 (late evening) 1 concentration on the control reaction (no

0.5

2000 0400
inhibition). [2]
0

t
0.5

1900 0500
1 b. State the initial rate of reaction at an ethanol

O
1.5

i
−3

2
concentration of 50 mmol dm in the presence of the
1800 (evening) 0600 (morning)

s
inhibitor at the following concentrations:

1700 0700

−3

i. 1 mmol dm [1]

y
1600 0800

−3

ii. 3 mmol dm . [1]

1500 (early aernoon) 0900 (late morning)

e
1000

p
1400 c. Explain the mechanism of competitive inhibition. [3]

1100
1300

1200 (mid-day)
v

3. A key reaction in photosynthesis occurs when ribulose

o
bisphosphate carboxylase (Rubisco) catalyses the fixation

a. Identify a time when c arbon dioxide uptake was

i

of carbon dioxide to ribulose bisphosphate (RuBP). To be

the same at both temperatures. [1]

effective, Rubisco must be activated by another enzyme

n

b. State the maximum rate of c arbon dioxide uptake

called activase. The activities of Rubisco and activase

at 15°C. [1]

(each isolated from tobacco leaves) were independently

U

c. Compare the rate of c arbon dioxide uptake at

investigated in a laboratory, under conditions of increasing
n

each temperature in daylight and in darkness. [3]

temperature.

d. Suggest why c arbon dioxide uptake is negative

a. State the
Key
o
d

at times. [1]
relationship isolated Rubisco

isolated activase

1–
3
1–

2. Alcohol dehydrogenase is an enzyme that c atalyses the between

gm
gm

6
i
r

Rubisco

ytivitca / ytivitca
ytivitca / ytivitca

reversible reaction of ethanol and ethanal according to

t

the equation below. activity and 2

o

temperature.
a

+ +

NAD + CH CH OH CH CHO + NADH + H

3 2 3

[1]
f

e s a v it c a
ethanol ethanal
o c s ib u r

2
u

b. C alculate the
x

The initial rate of reaction c an be measured according to

percentage

0
0
the time taken for NADH to be produced.
l

decrease
25 30 35 40 45 50
O

temperature / °C
In an experiment, the initial rate at different of activase
a

concentrations of ethanol was recorded (no inhibition). activity from the optimum temperature to 50°C. [1]
v

The experiment was then repeated with the addition

c. Determine which enzyme has the greater overall

−3

of 1 mmol dm 2,2,2-trifluoroethanol, a competitive

activity over the temperature range of 25 to 42°C. [1]
E

inhibitor of the enzyme. A third experiment using

d. Explain the observation of activase activity at

a greater concentration of the same inhibitor

temperatures higher than 42°C. [2]

−3

(3 mmol dm ) was also performed.

e. In a leaf, both enzymes are present together. Predict,

The results for each experiment are shown in the graph.

with a reason, how the rate of photosynthesis would

change from 35°C to 50°C. [2]

411
 I n t e ra c t i o n and

s
interdependence

s
e
r
2 Cells

y
l
I n t e ra c t i o n s between the individual components

n
of a s ys t e m result in the interdependence of the

t
components. In living s ys t e m s , the i n t e ra c t i o n s of the

O
i
individual components of the s ys t e m are i n t e g ra t e d . As a

s
result of this i n t e ra c t i o n and i n t e g ra t i o n , n ew properties

y
emerge at e ach level of biologic al organization,
e
including the cellular level. Even within multicellular

p
organisms, individual cells often h av e all of the emergent
v

properties a ss o c i a t e d with life such as homeostasis,

o
i

continuity between g e n e ra t i o n s , metabolism, materials

n

exc h a n g e with the e nv i r o n m e n t and i n t e ra c t i o n with

other cells. The image s h ow n is a toothbrush bristle

U

with dental plaque on its s u r f a c e. When bacterial

n

communities living on teeth re ach a certain d e n s i t y,

o

the signalling molecules they rele ase re ach a critic al

d

c o n c e n t ra t i o n le ading to the c o o p e ra t i v e production of

i
r

a matrix that prote cts the community f rom the b o d y ’s

t
o

defences.
a
f

u
x

l
O

a
v
E
C2.1 Chemic al signalling

LHA
How do cells distinguish between the many dierent signals they receive?

s
s
Signalling molecules bind to cellular receptors that

are either membrane bound or, in the c ase of steroid

e
hormones, in the cytoplasm of the cell. The receptors

r
have shapes that match certain signal molecules but

notothers.

y
▸ Figure 1 This Illustration shows ve transmembrane proteins with their

l
ligands (le to right): a potassium channel, a delta-opioid receptor, an LDL

n
(low-density lipoprotein) receptor, an acetylcholine receptor and a histamine

receptor. E ach channel or receptor is shown with its associated ligand: a

t
potassium ion (purple sphere), an endorphin molecule (shown in yellow), an LDL droplet

O
i
(spheric al lipid particle), an acetylcholine molecule (small pink molecule) and a histamine

molecule (orange)

s
r

y
e
What interactions occur inside animal cells in response to chemic al signals?

p
v

Cellular activity is regulated by chemic al signals, through

various mechanisms. Some of these mechanisms

o
i

involve signalling molecules binding to receptors in

n

the membrane, triggering a c asc ade of intracellular

responses.
U

▸ Figure 2 The orange sphere represents a chemic al signal.

n

It is shown attaching to a receptor (red) in the cell membrane (blue).

This c auses the receptor to bind to a G protein (yellow). A series of reactions

o
d

is triggered and the G protein activates a membrane enzyme c alled adenylate

cyclase (red, centre right). Further reactions involving cAMP (cyclic adenosine
i
r

monophosphate), various enzymes, and ATP (adenosine triphosphate), result in the

target protein (bottom right, yellow) being phosphorylated, controlling its activity
t
o

a
f

u
x

l
O

a
v
E

413
 Interaction and interdependence
LHA

C2.1.1 Receptors as proteins with binding

sites for specic signalling chemic als

Cells interact with each other by sending and receiving signals. Signals c an be

sent using a chemic al substance. Molecules of the chemic al signal are produced

s
by one cell and bind to receptors in another cell. Receptors are proteins, with

s
a site to which the signalling chemic al c an bind. Binding c auses changes in the

receptor, which stimulate a response to the signal by the target cell.

e
A molecule that binds selectively to a specic site on another molecule is known

r
as a ligand. The site on a receptor to which the signalling chemic al binds is

P
therefore its ligand-binding site. The selectivity or specicity of binding is similar

y
to enzyme–substrate specicity in enzymes:

l
• In both enzymes and receptors, binding of the ligand occurs at a specific site.

n
• The shape and chemic al properties of the ligand-binding site match those of

the ligand, preventing other substances from binding.

O
• Both enzymes and receptors are unchanged by the binding of a ligand, even

i
if there are temporary changes to induce fit.

s
There are also key dierences between enzymes and receptors.

y
• When a substrate binds to the active site of an enzyme, the substrate

▴ Figure 3 In this model, the adenosine

e
changes. It is converted chemic ally into the product and released. Another

receptor is shown in “wireform”, with the

p
substrate c an then bind to the active site, and this cycle c an repeat many

adenosine ligand pink (ribose) and green

v

times per second. Binding is very brief.

(adenine). The receptor is loc ated in the

plasma membrane, with an exposed pocket

• In contrast, a signalling chemic al may

o remain bound to a receptor for a long

i

that acts as the ligand-binding site. The

time bec ause the ligand-binding site does not act as a c atalyst and does
n

receptor is a single polypeptide with seven

not convert the signal chemic al into a product. The signalling chemic al is

alpha helices that straddle the membrane

eventually released unchanged.

U

n
o
d

i
r

t
o

active site substrate bound substrate converted products

f

vacant to active site to product released

u
x

l
O

a
v
E

▸ Figure 4 Enzymes

(top) and receptors

(bottom) both bind

a ligand, but the

ligand binding site binding causes a message is signalling chemical

outcome is dierent

vacant changes to the receptor conveyed to the cell released

414
 Cells

LHA
C2.1.2 Cell signalling by bacteria in

quorum sensing

A quorum is a xed number of individuals needed for a meeting to go ahead. For

example, in the UN Security Council, two-thirds of the members must be present at

s
any given meeting. A numerical count decides if there is a quorum. Other methods

s
have evolved to assess whether a population is large enough for a group activity,

for example, quorum sensing. This is based on intercellular communication and

e
has been observed in a wide range of bacteria. A switch in activity or behaviour is

triggered when the population density rises above a certain threshold.

r
P
In quorum sensing, signalling molecules are secreted at a low rate by all cells in the

y
population. These molecules diuse freely between cells and bind to receptors in

each cell. When there has been sucient binding of the signalling molecules to

l
receptors in a cell, gene expression is changed. This causes a switch in activities.

n
As population density rises, all cells receive more of the signalling chemic al from

O
other cells. Above a certain density, every cell in the population receives enough

i
to c ause the change in gene expression and the resulting switch in activity—they

s
have sensed that there is a quorum.

r
Quorum sensing is an example of interaction, bec ause signalling molecules

y
pass from cell to cell. The activities promoted by quorum sensing are examples
e

p
of interdependence, bec ause they are only eective if more than one cell

participates. For example, high densities of bacteria on teeth secrete glue-like

v

chemic als onto the tooth surface. Bacteria adhere (stick) to these chemic als in a

o
i

thin layer c alled a biolm. In other bacteria, bioluminescence is only switched on

when there is a high population density c apable of producing bright light.

n

Bioluminescence: An example of quorum sensing

U

Bioluminescence in the marine bacterium Vibrio scheri for luciferase to be produced. Light is not emitted, as it

was the rst c ase of quorum sensing to be discovered. would have no function and would be a waste of energy.
o
d

V. scheri cells produce and secrete a type of signalling

V. scheri forms a mutualistic relationship with various

molecule known as an autoinducer. The autoinducer

animal hosts such as the bobtail squid. In the squid, the
i
r

c an diuse between cells. It binds to a receptor protein

bacteria colonize a structure c alled the light organ. A
t

in the cytoplasm, known as LuxR. When this binding

high population density of the bacteria inside the light
o

has occurred, the LuxR–autoinducer complex binds to

organ leads to a high concentration of autoinducer, so
a

the DNA of V. scheri at a position where it induces the

bioluminescence is induced. The light emitted from the
f

transcription of genes. Expression of these genes results

u

squid helps to c amouage it in moonlight, reducing the

x

in the production of the enzyme luciferase.

risk of predation. Bacteria in the light organ are supplied

with sugar and amino acids by the squid.

l

O
O

O
O O
a
v

H
E

▴ Figure 5 The signalling molecule that acts as an autoinducer

of bioluminescence in Vibrio scheri

Luciferase catalyses an oxidation reaction that releases

◂ Figure 6

energy. Over 80% of this energy is transformed to greenish- Bioluminescence in the

blue light. Free-living V. scheri are at a low population bobtail squid Euprymna

berryi
density so they do not receive enough of the autoinducer

415
 Interaction and interdependence
LHA

C2.1.3 Hormones, neurotransmitters,

cytokines and c alcium ions as examples of

functional c ategories of signalling chemic al

s
in animals

s
Signalling chemic als in animals are very varied chemic ally, so they are usually

classied according to their function rather than their structure.

e
Hormones

r
Hormones are signalling chemic als produced in small amounts by a group of

y
specialized cells in the body and transported by the bloodstream. Organs that

are specialized for secretion are c alled glands. Most hormones are secreted into

l
blood c apillaries in the gland tissue. Bec ause of this internal secretion, glands

n
that secrete hormones are c alled endocrine glands. Exocrine glands have a duct

leading out of the organ to transport the secretion.

O
The bloodstream transports hormones to all parts of the body. However, they

i
only have eects on target cells which have receptors for the hormone. The

s
hormone regulates the activities of the target cells by promoting or inhibiting

r
specic processes. Hormones c an persist in the body for hours aer being

y
secreted, so the activities of target cells c an be aected for much longer than
e
with nerve impulses. Transport in the bloodstream means the secreting and

p
target cells c an be far apart and one hormone c an have very widespread eects.
v

o
Insulin, thyroxin and testosterone are example of hormones.
i

Neurotransmitters
n

Neurotransmitters are chemic als that transmit signals across synapses. A synapse
U

is a junction between two neurons in the nervous system: the presynaptic

neuron secretes the neurotransmitter and the postsynaptic neuron receives it.
n

The neurotransmitter is secreted when a nerve impulse reaches the end of the

presynaptic neuron. It diuses across the gap between the two neurons and
o
d

then binds to receptors in the plasma membrane of the postsynaptic neuron.

This binding inuences whether a nerve impulse is initiated in the postsynaptic

i
r

neuron. Excitatory neurotransmitters stimulate nerve impulses; inhibitory

t

neurotransmitters have the opposite eect.

o

The gap between the two neurons at a synapse is between 20 and 40 nanometres
f

and most neurotransmitters only travel this very short distance. This happens in
u
x

a fraction of a second, so neurotransmitters convey their signal far more quickly

than hormones. Neurotransmitters are rapidly broken down in the synaptic gap or
l
O

reabsorbed into the presynaptic neuron, so they only persist for a fraction of a second.
a

In consequence, their eects are short-lived. R apid removal of neurotransmitter from

the synaptic gap ensures it only aects one specic postsynaptic neuron; it does
v

not usually diuse out of the synapse to have more widespread eects.
E

Acetylcholine, norepinephrine and dopamine are examples of neurotransmitters.

Cytokines

Cytokines are small proteins that act as signalling chemic als. They are secreted by

a wide range of cells. The same cytokine may be secreted by dierent cell types

and one cell type may secrete several dierent cytokines. Certain cytokines c an

be secreted by almost all cells in the body.

416
 Cells

LHA
Cytokines are not usually transported as far as hormones. Instead, they act either

on the cell that produced them or on a nearby cell. Cytokines c annot enter cells

so they bind to receptors in the plasma membrane of a target cell. This binding

c auses c asc ades of signalling inside the target cell, leading to changes in gene

expression and thus in cell activity. One type of cytokine c an bind to several types

s
of receptor and so have multiple eects.

s
Cytokines have cell signalling roles in inammation and in other responses

e
of the immune system. They also have roles in the control of cell growth and

proliferation and in the development of embryos.

▴ Figure 7 Cytokines have c aused

r
Erythropoietin (EPO), interferon and interleukin are examples of cytokines. inammation in the region around a skin

P
infection as part of the body’s normal

y
C alcium ions
immune response. Sepsis is the poorly

understood and life-threatening condition

l
C alcium ions are used for cell signalling in both muscle bres and neurons.

in which interactions in the immune

n
system c ause a cytokine storm, leading to
In muscle bres, c alcium ions are pumped into a specialized form of endoplasmic

widespread organ failure

reticulum c alled the sarcoplasmic reticulum, generating a high concentration.

O
When the muscle bre receives a nervous impulse, c alcium channels open in

i
the membrane of the sarcoplasmic reticulum and the ions c an diuse out. They

s
bind to proteins that block muscle contraction, c ausing the proteins to change

position; this allows muscle contraction to occur. If the muscle bre does not

y
receive more nerve impulses, these changes are reversed and the c alcium is
e
pumped back into the sarcoplasmic reticulum.

p
v

In neurons, the arrival of a nerve impulse at a presynaptic membrane causes

o
calcium channels to open, allowing inward diusion. Inside the presynaptic
i

2+

neuron, C a ions cause secretion of neurotransmitter into the synaptic gap by

n

exocytosis. The calcium ions are rapidly pumped back out into the synaptic cle.
U

C2.1.4 Chemic al diversity of hormones and

n

neurotransmitters
o
d

Signalling systems using hormones and neurotransmitters have evolved

repeatedly and a wide range of chemic al substances have become signalling

i

chemic als. A signalling chemic al must:

r

• have a distinctive shape and chemic al properties so the receptor c an

o

distinguish between it and other chemic als

a

• be small and soluble enough to be transported.

f

u
x

Table 1 shows chemic al c ategories of hormone and neurotransmitter.

l
O

Hormones Neurotransmitters
a

Amines • melatonin Amines • dopamine

• thyroxin • norepinephrine
v

• epinephrine

Gases • nitrous oxide

E

Peptides • insulin

Amino acids • glutamate

• gluc agon

• glycine
• ADH

Steroids • oestradiol
Esters • acetylcholine

• progesterone

• testosterone

◂ Table 1

417
 Interaction and interdependence
LHA

Data-based questions: Nitrous oxide and mating in newts

The courtship of the crested newt (Triturus carnifex) involves the following stages:

1. male approaches female and snis her head

s
2. male waves his tail towards the female’s head

s
3. male hits female on her head with his tail

e
4. male deposits sperm next to the female

5. female picks up sperm.

r
A receptive female responds to the courtship by remaining motionless until picking up the sperm.

y
The male or female c an stop the courtship at any stage by moving away.

1. Using only the information given above, suggest ways in which:

l
y
a. the male c an nd out if the female is of the correct species [2]

n
b. the female c an decide whether or not to select the male for mating. [2]

O
Nitric oxide (NO) regulates

i
sexual behaviour in some
60

s
esahtnys edixo cirtin

animals. Newt brains contain

stinu yrartibra/ytivitca

nitric oxide synthase, which 50

y
c atalyses the formation of nitric
e
40
oxide. The amount of this enzyme

p
was measured in the brains of
v

30

male newts at various stages of

courtship. The results are shown

20
o
i
niarb

in Figure 8. (Source of data: Zerani

n

and Gobetti. 1996. Nature. Vol. 10

382. P 31.)
U

2. Outline the changes in the

n

amount of nitric oxide synthase before sniffing tail hitting sper aer

courtship waving head deposition copleting

in the male during the stages

courtship
of normal courtship and aer
o
d

stages of courtship
completing it. [3]
i
r

3. Using the data in the noral courtship

t

question, deduce the eects

straight aer a feale has stopped a courtship during one of its stages
o

of the female newt on nitric

a

15 inutes aer a feale has stopped a courtship during one of its stages

oxide levels in the brains of

f

male newts. [3]

u

▴ Figure 8 Source: Zerani, M., Gobbetti, A. Nature 382, 31 (1996). https://doi.

x

org/10.1038/382031a0.
l
O

ATL Communic ation skills: Responding to command terms

v

In experiments, when students propose a hypothesis, There can be more than one correct answer but not every
E

it is not certain that the hypothesis is correct. However, answer would be correct. Mark schemes for “suggest”

it is good scientic practice that there be some basis questions oen give the most likely hypothesis but also

for believing the hypothesis is correct. Sometimes a include the statement “or other reasonable suggestion”.

hypothesis is referred to as an “educ ated guess”. The emphasis is on the word “reasonable”—there should

be a basis for your “educated guess”.

Similarly, the command term “suggest” requires you to

propose a solution, hypothesis or other possible answer.

418
 Cells

LHA
C2.1.5 Loc alized and distant eects of
Activity: K aiten sushi

signalling molecules

In K aiten sushi, customers help

Some signalling molecules are only transported a very short distance and
themselves to sushi as it circulates

therefore have very loc alized eects. For example, neurotransmitters are released

s
on a conveyor belt. Are there any

by presynaptic neurons and may only have to diuse 20 nanometres to reach the
similarities with chemic al signalling

s
one postsynaptic neuron that they aect.
in the body?

e
Other signalling molecules are transported long distances in the body, from

the cells that secrete them to the target cells. Hormones are transported in the

r
blood from the gland that produces them to all parts of the body; the target

P
cells could be in any part of the body. For example, luteinizing hormone (LH) is

y
secreted by the pituitary gland adjacent to the brain. In males, the target cells

of LH are in the testes and in females they are in the ovaries, so the eects of this

l
hormone are very distant from its source.

n
t

O
▴ Figure 9

i
C2.1.6 Dierences between transmembrane

s
receptors in a plasma membrane and

y
intracellular receptors in the cytoplasm e
ornucleus

p
v

Signalling chemic als c an be divided into two groups, according to whether

o
they enter the target cell or not. Receptors for signalling chemic als that do pass
i

through the plasma membrane are loc ated in the cytoplasm or nucleus of the
n

cell; they are intracellular. Receptors for chemic als that do not penetrate are

loc ated in the plasma membrane of the target cell, with the binding site exposed

to the exterior. These receptors extend across the membrane with a region
U

extending into the cytoplasm; they are transmembrane receptors.

n

The loc ation of receptors is determined by the distribution of hydrophilic and

o

hydrophobic amino acids on the

d

surface of the receptor protein.

• Intracellular receptors have hydrophilic amino acids so they remain dissolved

i
r

in the aqueous fluids of the cytoplasm or nucleus.

t

• Transmembrane receptors have a band of hydrophobic amino acids on their

o

surface that is attracted to the apolar tails of phospholipids in the core of the

membrane. On either side of this band, there are hydrophilic amino acids
f

which are in contact with aqueous solutions inside and outside the cell.
x

l
O

a
v
E

▴ Figure 10 A gluc agon receptor (blue)

◂ Figure 11 Oestradiol (pink) binds to

with its position in the membrane shown by

the oestradiol receptor (blue). Pairs of

the grey slab. The hormone gluc agon binds

oestradiol–receptor complexes then jointly

to an extracellular protein (darker blue)

bind to DNA (orange and red), activating

which delivers it to the binding site on the

transcription of specic genes. Chains of

receptor

blue dots indic ate parts of the receptor that

are not shown in thisimage

419
 Interaction and interdependence
LHA

C2.1.7 Initiation of signal transduction

pathways by receptors

Binding of a signalling chemical to a receptor causes a sequence of interactions in

the cell, called a signal transduction pathway. These pathways are very varied as

s
they have evolved repeatedly, rather than having a common origin. Some signalling

s
chemicals such as proteins cannot pass through the plasma membrane; instead,

they bind to receptors in the plasma membrane. Other signalling chemicals, for

e
example steroids, pass through the membrane and bind to intracellular receptors.

Transmembrane and intracellular receptors use dierent transduction pathways.

r
P
When a signalling chemic al binds to the outer side of a transmembrane

y
receptor, it changes the structure of the receptor. The inner side of the receptor

becomes c atalytic ally active and c auses production of a secondary messenger

l
within the cell. This conveys the signal to eectors within the cell that c arry out

n
the responses.

O
Binding of signalling chemic als to intracellular receptors results in the formation

i
of an active ligand–receptor complex. In most c ases, this complex regulates

s
gene expression by binding to DNA at specic sites, promoting or inhibiting the

transcription of particular genes.

y
ligand approaches secondary messenger
e
the cell activates effectors

p
which carry out
v

responses to the signal

o
i

secondary
ligand binds to
n

messenger
transmembrane

produced
receptor
U

inside the cell

n

ligand
o
d

approaches ligand–receptor

the cell complex

i
r

regulates gene
t

expression
o

ligand passes into

a

the cell through

ligand binds to

the plasma
f

an intracellular
u

membrane
receptor
x

l
O

▴ Figure 12 An overview of signalling via transmembrane and intercellular receptors

v

Data-based questions: Treatments for

E

hypoglycemia

Hypoglycemia is low blood sugar concentration. In people with type 1

diabetes, severe hypoglycemia sometimes requires urgent treatment.

The hormones gluc agon and epinephrine c an both c ause blood glucose

concentration to increase in certain circumstances. Gluc agon is a protein and

epinephrine is an amine.

420
 Cells

LHA
Ten children with type 1 diabetes that was being treated with insulin were

−3

allowed to develop a blood glucose concentration of 2.8 mmol dm . Then

they were given injections of either epinephrine from an epipen or gluc agon.

The graphs in Figure 13 show the concentrations of these two hormones in

s
the children’s blood and the blood glucose concentration.

3,500

s
3,000
glucagon
3

e
md gn / nogaculg

epipen
2,500

r
2,000

P
1,500

y
1,000

l
500

n
0

O
5,000

i
3

s
md lomp / enirhpenipe

4,000

y
3,000
e

p
2,000
v

1,000

o
i
n

12
U

n
3

10
md lomm / esoculg

8
o
d

6
i
r

4
o

2
f

0
x

‒90 ‒75 ‒60 ‒45 ‒30 ‒15 0 15 30 45 60

l

time / min
O

▴ Figure 13 Source: T.P.C. Monsod et al;. Diabetes C are 1 April 2001; 24 (4): 701–704.

1. a. Compare and contrast the changes in gluc agon and epinephrine

v

following the injections. [3]

E

b. Deduce whether these changes are statistic ally signic ant. [1]

2. a. Discuss how rapidly a glucagon injection causes blood glucose

concentration to rise. [2]

b. Explain the processes that occur aer injection of gluc agon. [2]

3. Evaluate the use of epipens for treatment of hypoglycemia in children

with type 1 diabetes, using the data in the graphs. [2]

421
 Interaction and interdependence
LHA

C2.1.8 Transmembrane receptors for

neurotransmitters and changes to

membrane potential

s
Neurotransmitters convey signals between neurons, and between neurons

and muscle. Neurotransmitters are released into the synaptic gap and diuse

s
to the membrane of the postsynaptic neuron or the muscle bre. There, they

e
bind to receptors in these membranes. The receptors are transmembrane

proteins. Binding c auses membrane channels to open and ions move through

r
these channels by facilitated diusion, changing the membrane potential. This

change in potential is a signal that stimulates or inhibits either a nerve impulse in a

y
postsynaptic neuron, or a contraction in a muscle bre.

l
Acetylcholine is used as a neurotransmitter in many synapses, including those

n
between neurons and muscle bres. When acetylcholine binds to the binding

site on an acetylcholine receptor, the conformation (shape) of the receptor

t
changes. A channel opens, allowing sodium ions to pass into the cell. This leads

O
i
to a loc al depolarization that triggers an action potential. Synaptic transmission

s
and action potentials are described in Topic C2.2

y
e
C2.1.9 Transmembrane receptors that

p
v

activate G protein

G-protein-coupled receptors (GPCRs) are

o a large and diverse group of
i

transmembrane receptors. They convey signals into cells using a second

n

protein loc ated in the plasma membrane, c alled G protein. The three subunits

of G protein (α, β and γ) assemble on the receptor. A molecule of guanosine

U

diphosphate (GDP) bound to the α subunit keeps the G protein in an

n

inactivestate.

▴ Figure 14 Acetylcholine receptor

viewed from the side and from the end. When a ligand binds to the binding site on the receptor, the receptor changes
o
d

The binding site is shown in red and the

shape. This c auses changes in the coupled G protein, so the GDP detaches

membrane is shown in grey. The pore

from the α subunit. This allows guanosine triphosphate (GTP) to bind in its place.
i
r

through which sodium ions pass is only

Binding of GTP activates the G protein, which separates into its subunits and
t

open when acetylcholine is bound to

dissociates from the receptor. The activated G protein subunits c ause further
o

thereceptor
a

changes within the cell, triggering the cell’s response to the signal brought by

the ligand.
f

u
x

Resting state Binding of ligand Active state

l

outside
O

effector effector

γ γ γ
inside β
β β
v

α α
E

The alpha subunit A ligand binds to the receptor, causing The activated G protein

of the G protein is conformational changes which displace splits into alpha, beta and

inactive because GDP from the alpha subunit. gamma subunits which

GDP is bound to it. This allows GTP to bind, activating the convey signals to effectors

G protein. within the cell.

▴ Figure 15 Signal transmission into cells by G-protein-coupled receptors

422
 Cells

LHA
A broad range of receptor functions are mediated by G-protein-coupled

receptors and their associated G proteins. The ligands that bind to these

receptors are diverse and include light-sensitive compounds, odours,

pheromones, hormones and neurotransmitters.

s
s
Activity: Structure comparisons

e
1. a. Compare and contrast the structures of GTP c. Compare and contrast the structures of AMP

andATP. andcAMP.

r
b. Compare and contrast the structures of ATP

y
andAMP.

l
guanosine triphosphate adenosine-5’-triphosphate

n
O NH
2

N N
O O O O O O
NH N

O
HO P O P O P O HO P O P O P O

N N

i
N NH N
2
O O

OH OH OH OH OH OH

s
r
OH OH OH OH

y
e
adenosine monophosphate cyclic adenosine monophosphate

p
NH
NH
2
2
v

N
O
N C

o
N

C N
i

HO P O

N
N HC

O
n

C CH
OH

H N

2
N
O
C

O
HC CH

OH OH
U

P
n

O
O
OH
o
d

▴ Figure 16 Structures of GTP, ATP, AMP, cAMP

i
r

t
o

C2.1.10 Mechanism of action of epinephrine

a

(adrenaline) receptors
f

u
x

Epinephrine binds to a transmembrane receptor in the plasma membrane of

target cells. This changes the shape of the receptor, activ ating G protein within
l
O

the membrane. Activated G protein activates the enzyme adenylyl cyclase in

a

the membrane and this converts ATP in the cytoplasm into cyclic AMP (cAMP).

cAMP is the second or secondary messenger. Secondary messengers start a

v

sequence of responses within the cell, amplifying the signal until a large-sc ale

process is triggered. This happens very rapidly—for example, liver cells bre ak
E

down glucose and rele ase glucose into the blood within seconds of receiving

an epinephrine signal.

423
 Interaction and interdependence
LHA

2. receptor–hormone .  protein

complex formed activated

cytoplasm of

4. adenylyl cyclase

target cell

s
1. first activated

messenger

s
AT

(epinephrine)

. protein

diffuses to

e
inase
cA

receptor

activated
. second

r
by cA
messenger

P
. phosphorylase
(cyclic A)

y
inase activated
produced

by protein inase

l
. glycogen

n
phosphorylase

plasma membrane

activated by

t
of target cell

O
phosphorylase

i
inase

s
glucose
glycogen

r
phosphate

y
e
▴ Figure 17 Signal transduction pathway used in liver cells in response to epinephrine; this results in rapid release of

p
glucose into the bloodstream
v

Science as a shared endeavour: Naming conventions o

i
n

Naming conventions are an example of international non-proprietary (generic) name—in this c ase,

cooperation in science for mutual benet. Adrenaline and “epinephrine”. However, there is a risk of confusion with
U

epinephrine are the same hormone. The term “adrenaline” the stimulant drug ephedrine, so other people prefer the
n

relates to the adrenal gland, which produces the term “adrenaline”.

hormone. The term “epinephrine” refers to the position of

References
o

the adrenal gland—above (epi-) the kidney (nephros). The

d

James, RH. 1998. “Ephedrine/Epinephrine Drug L abel

chemical name of this hormone, based on the rules of the

Confusion”. Anaesthesia. Vol. 53. P 511.

International Union of Pure and Applied Chemistry, is (R)-1-
i
r

(3,4-dihydroxyphenyl)-2-methylaminoethanol. “‘Looks’ like a Problem: Ephedrine – Epinephrine.”

t
o

Institute For Safe Medication Practices, 17 Apr 2003,

In most of the world, the term “adrenaline” is more
a

https://www.ismp.org/resources/looks-problem-
common. However, “epinephrine” is more commonly
f

ephedrine-epinephrine.
used in North Americ a. Some people prefer to use a
u
x

l
O

C2.1.11 Transmembrane receptors with

a

tyrosine kinase activity

v

A kinase is an enzyme that adds a phosphate group from ATP to a specic

molecule. This process is called phosphorylation. For example, the enzyme

E

tyrosine kinase transfers phosphate from ATP to the amino acid tyrosine in a protein.

Look at Figure 18. The insulin receptor (blue) is a transmembrane protein that

is activated by the binding of insulin (orange). The two tails of the protein that

extend into the cytoplasm are tyrosine kinase enzymes The binding of insulin

c auses structural changes in the receptor, so the two tails connect to form a

dimer. Then each tail phosphorylates the other tail. These changes trigger

424
 Cells

LHA
a biochemic al chain of events inside the cell (signal transduction). Vesicles

containing glucose transporters move to the plasma membrane and fuse with

it, inserting transporters (shown in red) into the membrane. These transporters

are channel proteins that allow glucose (yellow) to enter the cell by facilitated

diusion. The glucose c an then be used as a substrate in cell respiration.

s
s
e
r
P

y
l
y

n
t

O
i
s
r

y
▴ Figure 18 Transmembrane insulin receptors
e

p
C2.1.12 Intracellular receptors that aect
v

gene expression
o
i

Steroid hormones are hydrophobic. This means they are soluble in lipids
n

and able to pass through the cell membrane. Once inside the cell, they bind

to receptors in the cytoplasm. The hormone–receptor complex enters the

U

nucleus and attaches to the DNA. This activates the production of a particular
n

polypeptide. For example, the androgen receptor binds testosterone and the

resulting complex increases production of the FADS1 gene. This in turn increases
o
d

production of important fats in prostate cells.

i
r

lipid-soluble
t

steroid hormone
o

nucleus

passes through
a

membrane

receptor
f

protein in
x

cytoplasm
hormone–receptor
l

complex attaches
O

to DNA

DNA
v
E

instructions for synthesis

of a polypeptide

cytoplasm
membrane of

◂ Figure 19 Signal transduction pathway

target cell polypeptide synthesized by

in cells that respond to steroidhormones

ribosomes and mRNA

425
 Interaction and interdependence
LHA

C2.1.13 Eects of the hormones oestradiol

and progesterone on target cells

The hormones oestradiol and progesterone are involved in reproduction.

s
Oestradiol has a broad range of eects in the ovary and the uterus. It also acts

s
on the brain, helping to regulate the release of reproductive hormones. Within

the hypothalamus of the brain, the hormone gonadotropin-releasing hormone

e
(GnRH) is produced and released. This hormone triggers the release of the sex

hormones luteinizing hormone (LH) and follicle-stimulating hormone (FSH) from

r
the anterior pituitary. At dierent stages of the human menstrual cycle, oestradiol

P
c an either inhibit or promote the release of GnRH by the hypothalamus. Just

y
before and during ovulation, oestradiol has a stimulating eect by binding to

a receptor within the cytoplasm of the hypothalamus cell. Once bound, the

l
hormone–receptor complex moves to the nucleus where it acts as a transcription

n
factor, enhancing the transcription of GnRH mRNA.

O
The hormone progesterone is produced by the ovary and maintains the uterine

i
lining so that it c an support a developing foetus. Progesterone is a steroid

s
hormone, able to diuse directly through the plasma membrane of uterine cells

and bind to a receptor in the cytoplasm. The hormone–receptor complex then

y
enters the nucleus where ite interacts with DNA as a transcription factor. This

aects gene expression. For example, one of the genes activated is insulin-

p
like growth factor which contributes to the cellular proliferation necessary for
v

maintaining the lining of the endometrium.

GnRH released by

hypothalamus
o
i
n

C2.1.14 Regulation of cell signalling

Release of FSH by
pathways by positive and negative
U

anterior pituitary
Just before and
n

feedback
during ovulation

In a positive feedback process, the end-product of a pathway

oestradiol stimulates
o
d

FSH binds to follicle

GnRH release amplies the starting point so that more product is created.

receptors, stimulating
For example, in muscle, the endoplasmic reticulum (ER) stores
i

follicle development
r

c alcium. The binding of an inositol trisphosphate (IP ) molecule

3
t

to an IP receptor c auses the partial release of c alcium from

3
o

2+

the ER. This increase in Ca activates the IP receptor on a

a

Follicle produces
neighbouring c alcium channel, c ausing further increases in
f

oestradiol 2+

Ca . This process is known as c alcium-induced c alcium release.

u
x

In a negative feedback process, an increase in the end-product

▴ Figure 20 An example of positive feedback

l

of a pathway shuts o the start of the pathway. In other words, the

O

2+
IP3
Ca
ER membrane
cytoplasm
v
E

ER lumen

▸ Figure 21 C alcium-induced c alcium

release

426
 Cells

LHA
end-product inhibits its own production. For example, testosterone production is

regulated by negative feedback. GnRH released by the hypothalamus acts on the

hypothalamus, stimulating the release of luteinizing hormone (LH). LH stimulates

the release of testosterone from Leydig cells in the testes. Increasing testosterone

levels have two eects:

s
• signals to the anterior pituitary decrease the release of LH

s
• signals to the hypothalamus stop the release of GnRH.

e
Exploring and designing: Testing a hypothesis

r
P
Bacteria in the mouth are in danger of being swallowed that stains dental plaque red or blue. This means they

y
and then killed by stomach acid. They c an prevent this c an be used to investigate the development or removal

by becoming attached to surfaces of the teeth and ofplaque.

l
y
gums. Glycoproteins in saliva adhere to the surface of
1. Suggest a hypothesis relating to factors aecting

n
teeth, allowing bacteria to attach and then multiply. The
development of plaque or methods of removal.

t
bacteria use quorum sensing to detect when a high

O
2. Design an experiment to test your hypothesis.

population density has developed. This triggers changes

i
3. Perform your experiment.
in gene expression. In particular, the bacteria secrete an

s
extracellular polysaccharide that forms a layer of slime
4. Use the results of the experiment to evaluate your

r
over the teeth; bacterial cells are immobilized in this slime.

y
hypothesis.

This type of biolm is known as dental plaque. It c an grow

e
thicker as more bacteria adhere and multiply and more

p
polysaccharide is secreted. Plaque formation has several
v

advantages for bacteria:

o
i

• less risk of being washed o the tooth

n

• harder for white blood cells, antibodies and other

antibacterials to penetrate and kill the bacteria

U

• dierent species of bacteria in the plaque c an interact

n

and benet from each other ’s activities.

Bacteria in dental plaque secrete acids, which react with

o
d

minerals in tooth enamel, c ausing dental dec ay. Removal

of plaque is therefore advisable.

i
r

Disclosing tablets c an be bought over the counter at

t

drug stores/pharmacies or online. They contain a dye

o

▴ Figure 22 Dental inspection to check for dec ay

a
f

u
x

Linking questions
l

1. What patterns exist in communic ation in biologic al 2. In what ways is negative feedback evident at all levels
O

systems? of biologic al organization?

a. Outline the process whereby heightened levels a. Explain the mechanisms involved in the
v

of glucose in the blood impact intracellular maintenance of body temperature. (D3.3.6)

signalling. (C2.1.11)
E

b. Outline the negative feedback control of

b. Explain the role of chemoreceptors in regulating population size by density-dependent factors.

ventilation rate. (C3.1.15) (C4.1.6)

c. O utline, using an example, how an individual c an c. O utline the role of negative feedback in one

signal reproductive tness during mate selection. example of cell signalling. (C2.1.14)

(D4.1.7)

427
 C2.2 Neural signalling

How are electric al signals generated and moved within neurons?

s
s
Neurons are cells within the nervous system that c arry

electric al impulses. As shown in Figure 1, each neuron has

e
a large cell body with structures extending from it. The

extensions usually consist of one thicker axon and several

r
thinner dendrites. In a living system, the dendrites collect

P
information. This information is interpreted by the cell

y
body and then passed on to the axon. How is a resting

l
electric al potential established? How is the nervous signal

y
transmitted down the length of the axon? How is the

n
neuron reset, ready for the next signal?

t
◂ Figure 1

O
i
s
How c an neurons interact with other cells?

y
Figure 2 shows the junction between a nerve cell
e
(green) and a muscle bre (red). Such junctions

p
are known as synapses. Neurons both receive
v

and transmit information from other cells. How do

o
neurons interact with sensory receptors? How do
i

they then transmit it to the dendrites of neurons?

n

The exchange of ions across axon membranes c an

lead to the transmission of electric al signals along

U

an axon. How is the signal transmitted between

◂ Figure 2

cells? What processes occur at the synapse?

n
o
d

i
r

t
o

a
f

u
x

l
O

a
v
E

428
 Cells

C2.2.1 Neurons as cells within the nervous

system that c arry electric al impulses

Two body systems are used for internal communic ation: the endocrine system

and the nervous system. The endocrine system consists of glands that release

s
hormones. The nervous system consists of nerve cells c alled neurons. There

s
are about 85 billion neurons in the human nervous system. Neurons help with

internal communic ation by transmitting nerve impulses. A nerve impulse is an

e
electric al signal.

r
Neurons have a cell body with cytoplasm and a nucleus. They also have narrow

P
outgrowths c alled nerve bres along which nerve impulses travel.

y
• Dendrites are short branched nerve fibres—for example, those used to

l
transmit impulses between neurons in one part of the brain or spinal cord.

n
• Axons are very elongated nerve fibres—for example, those that transmit

impulses from the tips of the toes or the fingers to the spinal cord.

O
i
s
cell body

axon

y
e

p
skeletal muscle (effector)

dendrites
v

o
i

▴ Figure 3 A motor neuron with dendrites that transmit impulses to the cell body and

an axon that transmits impulses a considerable distance to muscle bres (axon length not
n

to sc ale)
U

C2.2.2 Generation of the resting potential

n

by pumping to establish and maintain

o
d

concentration gradients of sodium and

i

potassium ions
r

If mi c ro e l e c t ro de s a re placed i n s i de and o u t s i de a ny l i vi n g cell, a vo l t a g e

o

a c ro ss th e me mbra n e will be d e t e c te d. This vo l ta ge is usually be tw e e n 10

and 1 0 0 mi l l i vo l t s ; it is k n ow n as th e me mb ra n e p o t e n ti a l . This po te n t i a l is due

f

to an i mb a l a n c e between the net c h a rge ( n e ga ti ve or p o s i t i ve) of c y to pl a s m

x

and the fluid o u t s i de. The cytoplasm of cells is ge n e ra l l y electric ally n e g a ti ve

l

c o m pa re d w i th the fluid o u ts i d e. Fo r th i s re a s o n , the me mb ra n e po te n t i a l

O

is ex pre ss e d as a n e ga ti ve v a l u e — fo r ex a mp l e, l i ve r cells h ave a po te n t i a l of

a

− 4 0 mV.
v

When a neuron transmits an impulse, its membrane potential changes suddenly.

When it is not transmitting an impulse, the potential across the membrane

E

usually remains close to −70 mV. This is c alled the resting potential. Three factors

contribute to it.

• Sodium–potassium pumps in the membrane transfer sodium ions (N a )

out of the neuron and at the s ame time transfer potassium ions (K ) in.

This is active transport and uses energy f rom ATP. The numbers of ions

429
 Interaction and interdependence

pumpe d are une qual: when thre e Na

0 mV

80 +40 ions are pumpe d out, only two K ions

mV mV
are pumpe d in. This c re ates a charge

imbalance and concentration gradients

voltmeter

for both ions.

electrode

s
outside
• The pumped ions leak back across the

s
the cell
fluid outside cell membrane by diffusion. The diffusion

rates are slow but the membrane is

e
about 50 times more permeable to

microelectrode
+ +

K than to Na . Therefore, leakage

r
inserted into
+

plasma of K ions is faster. This increases the

the cell

P
+ +

y
membrane difference between the Na and K

of cell concentration gradients, increasing the

cytoplasm

l
overall charge imbalance across the

y
membrane.

n
• There are negatively charged proteins

O
inside the nerve fibre (organic anions),

i
which also contribute to the charge

s
imbalance.

y
▴ Figure 4 Measuring membrane potential
e

p
v

o
fluid outside neuron
i

+
n

Na

Na +

Na
+

K
U

channel +

Na
+

closed
n

Na

Na

Na
o

+
d

Na

Na +

Na
i
r

t
o

+ +

Na /K
f

pump
x

l
O

+ +
+
K K
K

‒ channel

+
v

+ + closed
+
K K
Na
+
‒ K
‒
‒ +

‒ K
E

+
K ‒
K

‒
‒
‒ + +

+ K
K
K

‒ K
‒

K +
+
K
K
▸ Figure 5 The resting potential of a
protein
+

neuron is maintained by continual operation

of the sodium–potassium pump

cytoplasm

430
 Cells

Data-based questions: Energy for the sodium–potassium pumps in the brain

Sodium–potassium pumps establish and maintain the resting potential 18

in neurons of the brain. S amples of rabbit brain tissue were treated with
(6)

1–


s
ouabain, which inhibits the sodium–potassium ion pump. The oxygen

1–
gm μ / noitpmusnoc
consumption of the brain tissue was measured at dierent ouabain

s
(3)
concentrations. The graph in Figure 6 shows the results. Four of the

12

data points are mean values with error bars. The number of replic ates is

e
indic ated in brackets next to the data point. The other data points on the

r
graph are for concentrations where only a single measurement wastaken.
(3)

()

1. a. Outline the eect of ouabain at concentrations up to

y
−3
6
5 µmol dm , using data from the graph. [2]

n e g yx o
b. Explain this eect of ouabain, using your knowledge of

l
y
cell respiration and active transport. [3]

n
2. a. Outline the results of the experiment at ouabain concentrations

t
0
−3

between 5 and 10 µmol dm . [1]

O
5 10

i
–3
b. Deduce conclusions from the results between 5 and
concentration of ouabain / μmol dm

s
−3

10 µmol dm . [2]

▴ Figure 6
Source: R Whittam. Biochem J 1 January

r
1962; 82 (1): 205–212. doi: https://doi.

y
3. Use the data in the graph to estimate the proportion of energy

org/10.1042/bj0820205.

expenditure in rabbit brain tissue that is used by sodium–potassium pumps. [1]

e

p
4. At some ouabain concentrations, there were no replic ates; at other concentrations, there were only three.
v

Suggest a reason for this. [1]

o
i
n

C2.2.3 Nerve impulses as action potentials

U

that are propagated along nerve bres

n

Electrodes c an be used to monitor the membrane potential at one position

o

along a nerve bre. The potential c an be displayed on a screen, with time on the
d

x-axis and voltage on the y-axis. A horizontal line at about −70 mV represents the

resting potential. A sudden spike represents an action potential. This is an all-or-

i
r

nothing sequence of changes in membrane potential, with two

t

action potential peak

o

main phases:
a

+35
Vm /
ecnereffid

• depolarization—a change in membrane potential from

no

no
f

negative to positive
itaz
e n a rb m e m

itaz
u
x

0
iral

ira

• repolarization—a change back from positive to negative.

lop
op
l

laitnetop
O

ed

er

Both depolarization and repolarization are due to movement

a

ssorc a

threshold potential
of positively charged ions across the membrane—not to

–50

movement of electrons.
v

–70

restin potential
Depolarization is due to the opening of sodium channels in the
ndershoot
E

membrane, allowing Na ions to diuse into the neuron down

0 1 2 3 4 5 6 7
the concentration gradient. The concentration of sodium ions

time/ms

outside is about 10 times as high as that inside. The entry of

stimls
+

Na ions reverses the charge imbalance across the membrane,

so the inside is positive relative to the outside. The raises the

▴ Figure 7 Changes in membrane potential during an

membrane potential, typic ally from about −70 mV to a positive

actionpotential

value of about +30 mV.

431
 Interaction and interdependence

fluid outside neuron

+ + +

Na Na Na

Na +
+
Na
Na

K
channel +

s
+ Na

open + +

Na Na

s
+
+
Na
+ Na

Na +
+
Na

e
Na

r
P

y
+ +
+ Na /K
Na

l
pump

n
t
+ +
+
K K

O
Na

Na

i
‒
channel
+

+ +

s
K K closed

+
‒ ‒ K
+
‒
‒ K
+

r
+ K ‒

y
K

‒ ‒
‒ + +
+
+ K K
K
e
Na +
+
K
K
‒ ‒

p
+

Na

+
+ +
+ K
Na K
K
v

protein +
+

K Na

▸ Figure 8 Neuron depolarizing

cytoplasm
o
i
n

fluid outside neuron

U

+
+
Na + K
K
n

+
+
Na
K

channel K +

Na

+
o

+
closed
d

Na
Na

+ +

Na Na

+
i

+ K
r

+
K
K

+
t

+
K

K
o

a
f

+
u

K
+ +

Na /K
x

pump
l
O

+
+

K Na
+

K
v

‒
+

Na channel

+
+
K
Na
open
E

+
+
‒ ‒ K
+
K
Na
‒
‒
+ ‒
+ K

K
‒
+

‒ ‒ + K
+ +
K
+ Na
K
Na
‒

+ +

Na K
+
+
K
Na
protein

cytoplasm

▸ Figure 9 Neuron repolarizing

432
 Cells

Repolarization happens rapidly aer depolarization and is due to the closing

of the sodium channels and opening of potassium channels in the membrane.

Potassium ions diuse out of the neuron down their concentration gradient and

no more sodium ions diuse in. As a result, the inside of the neuron becomes

negative again relative to the outside. The potassium channels remain open until

s
the membrane potential has fallen to close to −70 mV.

s
The diusion of potassium repolarizes the neuron, but it does not fully restore

e
the resting potential as the concentration gradients of sodium and potassium

ions have not yet been re-established. This takes a few milliseconds of actively

+ +

r
pumping Na out and K in, before there c an then be another action potential.

P
Action potentials are propagated along nerve bres, bec ause the ion movements

y
that depolarize one part of the bre trigger depolarization in the neighbouring

part of the bre. This is how neural signals pass along nerve bres. A nerve

l
impulse is an action potential that starts at one end of a neuron and is propagated

n
along the axon to the other end of the neuron.

t
In humans and other vertebrates, nerve impulses always move in one direction

O
i
along neurons. This is bec ause an impulse c an only be initiated at one terminal

s
of a neuron and c an only be passed on to other neurons or dierent cell types

at the other terminal. Also, there is a refractory period aer a depolarization that

▴ Figure 10 Nerve impulses are electric al

y
prevents propagation of an action potential backwards along an axon.
but they do not involve movements of
e
electrons. Remember, electricity is energy

p
associated with any negatively or positively

C2.2.4 Variation in the speed of

v

charged particles, not just electrons

nerveimpulses
o
i
n

Nerve bres are circular in cross-section, with a plasma membrane enclosing

cytoplasm. In humans, the diameter is typic ally about 1 µm, although some nerve

bres are wider. Nerve impulses are conducted along nerve bres at a speed of
U

about 1 metre per second.

n

Some animals have nerve bres with larger diameters. An increase in diameter

reduces resistance, so impulses are transmitted along wider bres more quickly.
o
d

For example, giant axons in squid have a diameter up to 500 µm and conduct

impulses at 25 metres per second. These axons are used to coordinate a rapid
i
r

jet-propulsion esc ape response when a squid is in danger. Animals do not

t
o

have the space or resources for many giant axons, so they c an only use them to
a

coordinate actions where speed is vital. For example, earthworms have just three
f

giant axons that they use for an esc ape response to predator attacks.
u
x

Myelination is another modic ation of nerve bres that increases the speed

of nerve impulses. This is a coating of nerve bres that consists of a series of

l
O

Schwann cells, with gaps between c alled nodes of R anvier. In myelinated nerve
a

bres the nerve impulse c an jump from one node of R anvier to the next, speeding

up transmission along the nerve bre to as much as 100 metres per second.
v
E

myelin nucleus of node of

sheath Schwann cell Ranvier

◂ Figure 11 Detail of a myelinated nerve

bre showing the gaps between adjacent

axon Schwann cells (nodes of R anvier)

433
 Interaction and interdependence

s
s
e
r
P

y
▸ Figure 12 An electron micrograph of

l
y
the cut end of a nerve, which is a bundle of

n
axons. The outer coat of the nerve has been

removed. Myelin sheaths (purple) c an be

O
seen surrounding the axons (brown). The

i
magnic ation of the micrograph is ×2,000.

s
C alculate the range of diameters of the

axons, not including the myelin sheaths

y
around them
e

p
Data-based questions: Conduction velocities of
v

o
nerve bres and muscle
i
n

Table 1 gives data about the diameter of nerve bres and muscle and the

velocity of propagation of impulses.

U

−1

Type Diameter /µm Velocity / m s

n

1.0 1.3

Non-myelinated axons

1.5 2.0
o
d

Squid giant axon (non-myelinated) 500 25

5 30
i
r

Myelinated axons 12 70
t

20 120
o

Smooth muscle cells 5 0.05

f

C ardiac muscle cells 15 0.5

u

Skeletal (striated) muscle bres 50 6.0

x

▴ Table 1
O

1. Use an appropriate graph or chart to display the data in Table 1, so

that the relationship between diameter, myelination and velocity of

v

propagation c an be evaluated. [5]

E

2. Evaluate the evidence provided by the data for the hypothesis that:

a. there is a positive correlation between diameter and velocity of

propagation, and c alculate an r value to support your answer [3]

b. myelination increases the velocity of propagation of impulses. [2]

434
 Cells

Mathematics: The correlation coecient and the coecient of determination

The correlation coecient

1−
70

eht
In statistic al terms, a correlation is any statistic al

s m / evren

s
65
association. It most oen refers to the degree of line ar

fo
yticolev
association between a pair of variables. Correlation c an
60

s
be negative or positive as well as strong or we ak.

55

e
yrosnes
The correlation coecient (r) is a mathematic al tool used

n o i t c ud n o c
50

to determine the strength of a correlation. The closer the

r
absolute value of r is to 1, the stronger thecorrelation. 45

n a id e m

P
1. Figures 13 and 14 show the correlation between height
40

y
and the speed of conduction of two nerves found in

35

the arm, the median sensory nerve and the ulnar nerve.

l
30

n
a. State the type of correlation (positive or negative)

100 120 140 160 180 200

in each graph.

height / cm

O
b. Analyse the r values provided with respect to

i
▴ Figure 13 Body height and conduction velocity of the

conduction velocity versus height for the two

median sensory nerve in the arms of 37 people. r = −0.740,

s
nerves.

mean = 49.15 ± 8.11

y
The coecient of determination e
2

The coecient of determination ( R ) is a statistic

ranlu

p
70

designed to evaluate the degree to which variation

v

1−
eht

in the independent variable explains the variation in

60

o
s m /evren

the dependent variable. It c an be expressed as the

fo
i

50
yticolev

percentage of the variation in the dependent variable that

n

is explained by the variation in the independent variable.

40

Another way to explain it is that it represents the

yrosnes

30
n o i t c ud n o c
U

percentage of the data that is closest to the line of best

2
n

t. For example, for the data in Figure 13, R = 0.1523. 20

This means that only 15% of the variation in conduction

10

velocity is explained by the variation in height of the

o
d

subject; many of the data points are far from the line of 0

100 120 140 160 180 200

best t. If the line of best t passed through every point of
i
r

2 height / cm
the sc atter plot, R would be 1 and the variation in height
t

would explain all of the variation in conduction velocity.

o

▴ Figure 14 Body height and conduction velocity of the

a

ulnar sensory nerve in the arms of 37 people. r = −0.220,

2. The data points in Table 2 represent the relationship

mean = 46.67 ± 10.62

f

between conduction velocity and axon diameter

u

Source of Figures: Sulaxane, Y. and Bhavasar, R. (2017). National Journal of

inmammalian nerves that are surrounded by a
x

Physiology, Pharmacy and Pharmacology, p. 1. Available at: https://doi.

myelinsheath.
org/10.5455/njppp.2017.7.0410317042017.
l
O

–1 –1

Axon diameter / μm Conduction velocity / m s Axon diameter / μm Conduction velocity / m s

a

2.1 9 6.5 38
v

2.2 15 11.0 53

3.0 10 12.8 81
E

2.8 17 12.9 82

16.1 98 13.0 86

20.0 120 8.0 41

14.0 70 13.9 76

10.0 58 10.3 51

▴ Table 2

435
 Interaction and interdependence

Follow these steps to nd the correlation coecient: • Press return and the r value will appear in the cell.

• Enter the data into a spreadsheet program.

Use a suitable soware program to graph the data points.

Choose a sc atter plot to represent the data. Add a

• Click in an empty cell where you would like the r value

trendline and click in the box indic ating that R should be

to appear.

s
shown.

• From the functions menu, choose “CORREL” and

a. Determine the r and R values.

s
then highlight the rst column. The associated range

should appear in the r value cell. Add a comma, then b. Analyse the r value.

e
highlight the second column.
2

c. Analyse the R value.

r
P

y
Collecting and processing: C alculating reaction time

l
y

n
The speed of transmission of nerve impulses allows rapid reaction time, such as the eect of auditory distraction or

t
responses to stimuli. A simple method of measuring whether the subject has one or both eyes open. Variables

O
reaction time involves dropping a ruler. must be c arefully controlled.

i
Two students working together c an assess reaction time. Reaction time, t, c an be c alculated using the formula:

s
The subject rests their elbow on a table with their hand 2d

t =

r
extended over the edge. The other student holds a metre g

y
stick with the 0 cm mark between the subject’s thumb −2

where g is the acceleration due to gravity (980 cm s ) and

e
and index nger. They let go of the ruler and the subject

p
d is the distance measurement from the ruler.

attempts to c atch it as quickly as possible.

v

Computer-based reaction timers are also available. You

The distance the ruler falls gives a measure of reaction

o
c an nd these by searching for “online reaction timer ”.
i

time. This allows investigation of factors that might aect

Compare and contrast the results from the two methods.

n

C
U

C2.2.5 Synapses as junctions between

n

neurons and between neurons and

o
d

eectorcells
i

A synapse is a junction between two cells in the nervous system. There are three
r

main types of junction.

t
o

• synapses between sensory receptor cells and neurons, in sense organs

a

• synapses between neurons, in both the brain and spinal cord

f

u
x

• synapses between neurons and muscle fibres or gland cells. Muscles and

glands are c alled effectors, bec ause they effect (c arry out) a response to
l

astimulus.
O

Signals c an only pass in one direction across a synapse. The presynaptic neuron
v

brings the signal to the synapse in the form of a nerve impulse or action potential.

The postsynaptic neuron c arries the signal away from the synapse, again in the
E

form of a nerve impulse. Chemic als c alled neurotransmitters c arry signals across

a narrow uid-lled gap between the presynaptic and postsynaptic neurons. This

gap is only about 20 nm wide.

436
 Cells

C2.2.6 Release of neurotransmitter from a

presynaptic membrane

Synaptic transmission occurs very rapidly as a result of these events:

s
• A nerve impulse is propagated along the presynaptic neuron until it reaches

the end of the neuron and the presynaptic membrane.

s
2+

• Depolarization of the presynaptic membrane c auses c alcium ions (C a ) to

e
diffuse through channels in the membrane into the neuron.

2+

• Influx of Ca c auses vesicles containing neurotransmitter to move to the

r
presynaptic membrane and fuse with it.

y
• Neurotransmitter is released into the synaptic gap by exocytosis.

l
y
presynaptic
nerve

n
neuron
impulse

O
▴ Figure 15 Electron micrograph of

i
a synapse. F alse colour has been used

s
synaptic knob to indic ate the presynaptic neuron (red)

2+

Ca diffuses
with vesicles of neurotransmitter (purple)

y
into knob
e and the postsynaptic neuron (green). The

synaptic gap (orange) is very narrow. The

synaptic vesicles

p
slight swelling at the end of the presynaptic

neuron is c alled the synaptic knob

v

presynaptic

membrane
o
i

neurotransmitter
n

synaptic gap

20 nm approximately

receptor
U

ion channel opened

o
d

postynaptic
i

membrane
r

t
o

postsynaptic neuron
a
f

u
x

▴ Figure 16 A nerve impulse is propagated across a synapse by the release of

neurotransmitter, followed by diusion and binding to receptors

l
O

a
v

C2.2.7 Generation of an excitatory

postsynapticpotential
E

Release of neurotransmitter from a presynaptic neuron leads to a series of events

that trigger an action potential in the postsynaptic neuron.

• Neurotransmitter molecules diffuse across the synaptic gap. This happens

extremely rapidly bec ause the distance is so short (20–40 nm). The gap

between the membranes is only two to four times the thickness of a typic al

phospholipid bilayer.

437
 Interaction and interdependence

• The neurotransmitter binds to receptors in the postsynaptic membrane,

c ausing ion channels to open. Some receptors have an ion channel as part of

their structure. Other receptors c ause an ion channel to open in a separate

membrane protein.

• Ions diffuse down their concentration gradient into the postsynaptic neuron,

s
c ausing the membrane potential to change. In most c ases, the potential rises

s
(becomes less negative)—this is c alled an excitatory postsynaptic potential.

e
• If the excitatory postsynaptic potential is strong enough, it triggers an action

potential which propagates away from the synapse.

r
• The neurotransmitter is rapidly broken down and removed from the

P
synaptic gap.

y
M any dierent neurotransmitters are used at synapses, with dierent eects.

l
For example, acetylcholine is used as the neurotransmitter in many synapses,

n
including neuromuscular junctions (synapses between neurons and muscle

bres). In the presynaptic neuron, choline (absorbed from the diet) is combined

O
with an acetyl group produced by aerobic respiration. This produces

i
acetylcholine, which is loaded into vesicles and then released into the synaptic

s
gap during synaptic transmission.

y
When acetylcholine e binds to its receptor in the postsynaptic

membrane, a channel opens in the receptor. Sodium ions diuse

p
through this channel and into the postsynaptic membrane, c ausing an
v

excitatory postsynaptic potential.

o
The acetylcholine only remains bound to the receptor for a short time
i

and only one action potential is initiated in the postsynaptic neuron. This
n

is because the enzyme acetylcholinesterase is present in the synaptic

choline gap and rapidly breaks acetylcholine down into choline and acetate. The
U

choline is reabsorbed into the presynaptic neuron, where it is converted

n

back into acetylcholine by recombining with an acetyl group.

▴ Figure 17 Acetylcholine
o
d
LHA

C2.2.8 Depolarization and repolarization

i
r

during action potentials

t
o

Opening of the sodium and potassium channels that c ause depolarization and

repolarization is triggered by changes in the transmembrane voltage. This is

f

c alled voltage-gating. If the resting potential of −70 mV increases to −50 mV,

x

sodium channels in the membrane start to open. This allows sodium ions to

diuse into the axon, further reducing the membrane potential and c ausing more
l
O

sodium channels to open. This is an example of positive feedback and c auses the
a

very rapid change in membrane potential from −50 to +30 mV that characterizes

depolarization during an action potential.

v

The voltage that causes sodium channels to open is called the threshold potential.
E

Depolarization will not occur unless the threshold potential is reached; instead, the

sodium–potassium pump will re-establish the resting potential of −70 mV. A nerve

impulse is “all-or-nothing” because the threshold potential must be reached.

Sodium channels remain open for a very short time—one to two milliseconds—

before they close again. Their opening allows a pulse of sodium ions to diuse

out. The resulting depolarization c auses voltage-gated potassium channels to

438
 Cells

LHA
open. These channels also remain open for one to two milliseconds, before

closing. Even in this short time, enough potassium ions diuse out of the axon to

repolarize the axon. The membrane potential returns to −70 mV; it may briey

become more negative than this, before the sodium–potassium pump re-

establishes concentration gradients.

s
1 channel closed 2 channel briefly open net negative charge

s
e
+ + + + + + + + outside

+
+
+
+
+

r
+
+
+

y
+
+
+ +
+ + +
+

inside of axon
‒ ‒ ‒ ‒ ‒ ‒ ‒ ‒ ‒

l
chain

y
net negative charge inside

n
+ net positive
K ions
ball the axon and net positive

charge

t
charge outside

O
i
s
3 channel closed by "ball and chain"

r
◂ Figure 18 Depolarization of the

y
axon c aused by inward diusion of
e
+ +

+ + Na c auses a conformation change,

p
+ +

+ + opening the potassium channel and

v

allowing outward diusion, which

o repolarizes the axon (stage 2). Aer

i

a few milliseconds, the protein ball

n

attached to the potassium channel

blocks it (stage 3). The channel

hydrophobic core hydrophilic outer

then returns to its former closed

U

of the membrane parts of the membrane

conformation (stage 1)
n
o
d

C2.2.9 Propagation of an action potential

along a nerve bre/axon as a result of

i
r

loc alcurrents
o

The propagation of an action potential along an axon is due to movements of

sodium ions. Depolarization of part of the axon is due to diusion of sodium

f

ions into the axon through sodium channels. This reduces the concentration of
x

sodium ions outside the axon and increases it inside. The depolarized part of the
l

axon therefore has dierent sodium ion concentrations to the neighbouring part
O

of the axon that has not yet depolarized. As a result, sodium ions diuse between
a

these regions both inside and outside the axon.

v

Inside the axon, there is a higher sodium ion concentration in the depolarized

part of the axon. As a result, sodium ions diuse along inside the axon to the
E

neighbouring part that is still polarized. Outside the axon, the concentration

gradient is in the opposite direction so sodium ions diuse from the polarized

part back to the part that has just depolarized. These movements are c alled loc al

currents (see Figure 19).

Loc al currents reduce the concentration gradient in the part of the neuron that

has not yet depolarized. This makes the membrane potential rise from the

439
 Interaction and interdependence
LHA

resting potential of −70 mV to about −50 mV. Sodium channels in the axon

membrane are voltage-gated and open when a membrane potential of −50 mV is

reached. This is the threshold potential. Opening of the sodium channels c auses

depolarization. Thus loc al currents c ause a wave of depolarization and then

repolarization to be propagated along the axon at a rate between 1 and 100

s
(or more) metres per second.

s
▾ Figure 19 Loc al currents

e
impulse movement

r
P

y
+
d iff u sio
a n

l
N

n
outside

t
inside

O
i
membrane

+
N
a n
io
diffus

s
r

y
e

p
part that has just depolarized part that has not yet depolarized

(action potential) (resting potential)

v

o
i
n

C2.2.10 Oscilloscope traces showing resting potentials and action potentials

Membrane potentials in neurons c an be

U

measured by placing electrodes on each

n

side of the membrane. The potentials

c an be displayed using an oscilloscope.

o
d

The display is similar to a graph with

time on the x-axis and the membrane

i
r

potential on the y-axis. If there is a resting

t

potential, a horizontal line appears on the

o

oscilloscope screen at a level of −70 mV

a

(assuming this is the resting potential of

f

the neuron). If an action potential occurs,

u
x

a narrow spike is seen. The rising and

falling phases of this spike show the

l
O

depolarization and repolarization.

a
v

▴ Figure 20 Oscilloscope showing a trace with action potentials

E

440
 Cells

LHA
Data-based questions: Analysing an oscilloscope trace

The oscilloscope trace in Figure 21 was taken from a digital oscilloscope. It

shows an action potential in a mouse hippoc ampal pyramidal neuron that

s
happened aer the neuron was stimulated with a pulse of current.

s
Vm /

50

e
eg at l o v

r
0
e n a rb m e m

y
resting potential

50

l
y

n
0 50 100

t
time / ms

O
i
▴ Figure 21 Oscilloscope trace taken from a digital

s
oscilloscope, showing an action potential in a mouse

hippoc ampal pyramidal neuron aer it was stimulated

y
with a pulse of current
e

p
1. State the resting potential of the mouse hippoc ampal
v

pyramidal neuron. [1]

2. Deduce the threshold potential needed to open voltage-gated sodium

o
i

channels in this neuron. Give a reason. [2]

n

3. Estimate the time taken for the depolarization, and the repolarization. [2]
U

4. Predict the time taken from the end of the depolarization for
n

the resting potential to be regained. [2]

5. Discuss how many action potentials could be stimulated per

o

second in this neuron.

d

[2]

6. Suggest a reason for the membrane potential rising briey

i
r

at the end of the repolarization. [1]

t
o

a
f

C2.2.11 S altatory conduction in myelinated

u
x

bres to achieve faster impulses

l
O

The basic structure of a nerve bre along which a nerve impulse is transmitted is
a

very simple: the bre is cylindric al in shape, with a plasma membrane enclosing

a narrow region of cytoplasm. The diameter in most c ases is about 1 µm, though
v

some nerve bres are wider than this. A nerve bre with this simple structure

conducts nerve impulses at a speed of about 1 metre per second.

E

Myelination of nerve bres is described in Section C2.2.4. Myelin is multiple

layers of phospholipid membrane that are deposited around the nerve bre, as

Schwann cells grow round and round it. E ach time they grow around the nerve

bre a double layer of phospholipid bilayer is deposited. There may be 20 or

more layers when the Schwann cell stops growing.

441
 Interaction and interdependence
LHA

The myelin sheath prevents ion movements, so action potentials only

occur at nodes of R anvier. Sodium–potassium pumps and both sodium

and potassium channels are clustered at nodes, with very few where the

axon is coated in myelin. Loc al currents allow the nerve impulse to jump

from one node of R anvier to the next. This is c alled saltatory conduction

s
and gives speeds of transmission of the nerve impulse as high as

100metres per second.

s
e
C2.2.12 Eects of exogenous chemic als

r
on synaptic transmission

y
An exogenous chemic al is one that enters the body of an organism from

l
an outside source. These chemic als c an enter through the skin, the

n
lungs or the gut, or they c an be injected. Some exogenous chemic als

aect synaptic transmission, either by blocking it or by promoting it. Two

t
examples are described here.

O
i
▴ Figure 22 Transverse section of axon

Neonicotinoids
showing the myelin sheath (red) formed

s
by the Schwann cell's membrane wrapped
Neonicotinoids are synthetic compounds similar to nicotine. They bind to the

r
round the axon many times. The cytoplasm

y
acetylcholine receptor in cholinergic synapses in the central nervous system

of the Schwann cell (green) contains

of insects. Acetylcholinesterase does not break down neonicotinoids, so

e
mitochondria (orange)

p
the binding is irreversible. Bec ause the receptors are blocked, acetylcholine
v

is unable to bind and synaptic transmission is prevented. This leads to

o
paralysis and death of the insects. Neonicotinoids are therefore very eective
i

Activity: Updates on insecticides.

n

neonicotinoids
One of the advantages of neonicotinoids as pesticides is that they are not highly

toxic to humans and other mammals. This is bec ause insects have a much greater
U

There are currently intense research

proportion of cholinergic synapses in their central nervous system, compared

eorts to try to discover whether

n

with mammals. Neonicotinoids also bind much less strongly to acetylcholine

neonicotinoids are to blame for

receptors in mammals than insects.

collapses in honeybee colonies.

o
d

What are the most recent research Neonicotinoid pesticides are now used on huge areas of crops. One

ndings and do they suggest neonicotinoid in particular, imidacloprid, is the most widely used insecticide
i
r

that these insecticides should in the world. However, concerns have been raised about the eects of these
t

bebanned? insecticides on other non-pest species. This has led to considerable controversy
o

and the evidence of harm is disputed by the manufacturers and some

government agencies.
f

u
x

Coc aine
l

Coc aine acts at synapses that use dopamine as a neurotransmitter. It binds to

O

dopamine reuptake transporters, which are membrane proteins that pump

a

dopamine back into the presynaptic neuron. Bec ause coc aine blocks these
v

transporters, dopamine builds up in the synaptic gap and the postsynaptic

neuron is continuously excited. Coc aine is therefore an excitatory or stimulant

E

psychoactive drug that gives feelings of euphoria that are not related to any

▴ Figure 23 Bumblebees on an

particular reward activity (such as eating).

Allium ower

442
 Cells

LHA
Activity: Cholinergic receptor ligands

C an you se e any mole cular similarities that explain why all these structures

c an bind to acety lcholine re ceptors?

s
CH
O 3

s
+
N CH
3

H C N
3

e
CH
3

CH
acetylcholine 3

r
N

nicotine

y
NO CN
2

l
y
N N

n
t
N N S
NH

O
i
s
CI N CI N

imidacloprid thiacloprid

y
▴ Figure 24 The molecular structures of acetylcholine, nicotine and two
e
neonicotinoids: imidacloprid and thiacloprid

p
v

o
i

C2.2.13 Inhibitory neurotransmitters and IPSP

n

generation of inhibitory postsynaptic

U

potentials
n

EPSP

Not all neurotransmitters stimulate action potentials in the postsynaptic neuron.

When some neurotransmitters bind to the postsynaptic membrane, the

o
d

membrane potential becomes more negative. This hyperpolarization makes it

more dicult for the postsynaptic neuron to reach the threshold potential. Nerve
i

EPSP plus IPSP

r

impulses are inhibited, rather than stimulated.

t
o

GABA (γ-aminobutyric acid) is an inhibitory neurotransmitter. When it binds

a

to its receptor a chloride channel opens, c ausing hyperpolarization of the

f

postsynaptic neuron by entry of chloride ions. In contrast, acetylcholine is an

u

action
x

excitatory neurotransmitter bec ause it c auses entry of positively charged ions to

EPSPs potential
the postsynaptic neuron, reducing polarization.
l
O

Transient changes to membrane potential c aused by neurotransmitters such as

GABA and acetylcholine are known as inhibitory and excitatory postsynaptic

v

potentials. Figure 25 shows single inhibitory and excitatory potentials and

possible eects of combined potentials. action potential

E

IPSP

EPSPs

▸ Figure 25 Sketches of typic al oscilloscope traces for

single inhibitory (IPSP) or excitatory postsynaptic potentials

100 ms
(EPSPs) and combinations of potential

443
 Interaction and interdependence
LHA

C2.2.14 Summation of the eects of

excitatory and inhibitory neurotransmitters in

a postsynapticneuron

s
More than one presynaptic neuron c an form a synapse with the same

postsynaptic neuron—especially in the brain, where there may be hundreds or

s
even thousands of presynaptic neurons. Usually a single release of excitatory

e
neurotransmitter from one presynaptic neuron is insucient to trigger an

action potential, bec ause one excitatory postsynaptic potential does not

r
reach the threshold potential. Either one presynaptic neuron must repeatedly

release neurotransmitter, or several adjacent presynaptic neurons must

y
release neurotransmitter more or less simultaneously. When multiple releases

of excitatory neurotransmitter combine to c ause an action potential, this is

l
c alledsummation.

n
Summation c an also combine the eects of inhibitory and excitatory

t
neurotransmitters. Whether or not an action potential is initiated in the

O
i
postsynaptic neuron depends on the balance between the eects of these

s
two types of neurotransmitter. Inhibitory neurotransmitters counter the eects

of excitatory neurotransmitters so the threshold potential is not reached. The

▴ Figure 26 Climbers heading for a

y
summit must decide whether to continue threshold potential will only be reached if there are many more excitatory

or descend. They will consider factors such

e
neurotransmitters than inhibitory neurotransmitters.

p
as weather conditions, tiredness, hours

The synapses integrate signals from many dierent sources. This is the basis of
of daylight and proximity to the summit,
v

before making the binary decision decision-making processes in the central nervous system.

o
i
n

C2.2.15 Perception of pain by neurons with

U

free nerve endings in the skin

n

Pain receptors in the skin and other parts of the body detect stimuli such as the

chemic al substances in a bee’s sting, excessive heat or the puncturing of skin by

o
d

a hypodermic needle. These receptors are the endings of sensory neurons that

convey impulses to the central nervous system. The nerve endings associated
i
r

with pain receptors have channels for positively charged ions. These channels
t

open in response to a stimulus such as high temperature, acid or certain

o

chemic als (such as c apsaicin in chili peppers). Entry of positively charged ions

c auses the threshold potential to be reached and nerve impulses then pass
f

through the sensory neuron to the spinal column. Interneurons in the spinal cord
x

relay the impulse to the cerebral cortex.

l
O

When impulses reach sensory areas of the cerebral cortex, we experience the
a

sensation of pain. Signals are transmitted to the prefrontal cortex, allowing us to

become fully aware of the pain and evaluate the situation. This will oen result
v

in a signal from the brain to the eectors of behaviour, reducing exposure to the

stimulus. For example, you might move your hand away from a hot surface.
E

◂ Figure 27 C arolina Reaper chillies (Capsicum

chinense) are among the “hottest”. They have very

high concentrations of c apsaicin, which gives a

sensation of heat or burning when eaten

444
 Cells

LHA
Communic ation skills: Taking c are with word choice

Equivoc ation involves treating words as though they have the same meaning,

when they do not. This is a common mistake made by ToK students who use

s
the terms perspective and perception interchangeably. Another language

error is to use metaphors which misrepresent mechanisms. For example, a

s
student might say that the nucleus is the “control centre” of the cell, but this

e
implies that DNA has an active role in cellular metabolism. In fact, DNA is a

relatively inert molecule and depends on other molecules interacting with it.

r
Taxonomists sometimes make mistakes in their naming that c an lead to

misunderstanding. The jalapeno pepper ( Capsicum annuum) is not an

y
annual plant as it c an grow for more than one year. The habanero pepper

(Capsicum chinense) is native to the Americ as not China, so this species name

l
is misleading.

n
C. annuum and C. chinense can be used to illustrate another situation where

t
words must be chosen carefully. The seeds of these plants contain the chemical

O
capsaicin, which is released by chewing and causes intense pain in the mouth.

i
An animal that chews the seeds when eating jalapeno or habanero peppers kills

s
the seeds and senses pain. An animal that swallows without chewing the seeds

does not experience pain and the seeds pass through the gut undamaged, to

y
be egested in faeces. The seeds are dispersed and provided with fertilizer from
e
the faeces. Mammals including humans chew, but birds do not.

p
The teleologic al view is that nature has denite intentions or purposes. These
v

are teleologic al statements:

• Habanero peppers are “designed” so the seeds are not killed by chewing.
o
i
n

• The pepper “wants to be eaten” by a bird.

• Humans “are not meant to eat the seed”.

U

• Peppers make c apsaicin “to stop mammals chewing their seeds”.

n

Critics of teleologic al viewpoints argue that evolution by natural selection is

not a directed process. Instead, mutations arise by chance and mutations that
o
d

give an advantage are more likely to persist in the population.

i
r

t
o

C2.2.16 Consciousness as a property that

a

emerges from the interaction of individual

f

u
x

neurons in the brain

l

If we are conscious of something, we are aware of it. We do not have to be

O

actively thinking about something to be aware of it, so we c an be simultaneously

aware of many things. This state of complex awareness is known as

v

consciousness. There is agreement that it exists, but philosophers and scientists

have not yet agreed on how to dene it.

E

Sleep is a state of reduced or partial consciousness. General anaesthetics, used

during surgery, make us unconscious. However, scientists do not fully understand

how these drugs work, so they do not reveal much about the physiologic al

basis of consciousness. Perhaps the most we c an say with certainty is that

consciousness emerges from the interaction of individual neurons in the brain: it

is an example of an emergent property.

445
 Interaction and interdependence
LHA

An emergent property is c aused by interactions between the elements of a

system. It is not a property of any one component; rather, it is a property of the

system as a whole. When we recognize that a system is more than the sum of

its parts, we are acknowledging the existence of emergent properties. Two

biologic al examples are the c atalytic activity of enzymes and ight in birds.

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▴ Figure 28 Auguste Rodin’s sculpture “Le Penseur ”—a study

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Linking questions
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1. In what ways are biologic al systems regulated?

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a. Describe an example where the concentration of a chemic al in the

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blood triggers a homeostatic mechanism. (D3.3.1)

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b. Explain the role of negative feedback in enzyme function. (C1.1.16)

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c. Explain the role of nerves in regulating a body system. (C3.1)

2. How is the structure of specialized cells related to function?

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a. Outline the role of proteins in nerve function. (C2.2.2)

b. Distinguish between the structure and function of type I and type II

pneumocytes. (B2.3.8)

c. Compare and contrast the functions of phagocytes and lymphocytes.

(C3.2)

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What challenges are raised by the

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dissemination and/or communic ation of

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scientic knowledge?

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L anguage presents challenges to scientists as they try to Some names have arbitrary origins. For example, the