NATURE OF BIOLOGY Book 2 THIRD EDITION JUDITH KINNEAR MARJORY MARTIN
This edition published 2006 by
John Wiley & Sons Australia, Ltd
42 McDougall Street, Milton, Qld 4064
Offi ces also in Sydney and Melbourne
Typeset in 10.5/12 pt Times
First edition published 1992
Second edition published 2000
© Judith Kinnear and Marjory Martin 1992, 2000, 2006
The moral rights of the author have been asserted.
National Library of Australia
Cataloguing-in-publication data
Kinnear, J. F. (Judith F.).
Nature of biology. Book 2.
3rd ed.
Includes index.
For year 12 students in Victoria.
ISBN-13 978 0 7314 0239 7.
ISBN-10 0 7314 0239 1.
1. Biology — Textbooks. I. Martin, Marjory. II. Title.
570
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CONTENTS 5
CONTENTS
Preface xii
About the CD-ROM xiii
Acknowledgements xiv
1 The chemical nature of cells 2
Examining molecules 3
Biotech: The Australian Synchrotron 3
Water: a unique compound 4
Organic molecules 8
Carbohydrates — energy rich 9
Proteins 14
Forensics — detecting haemoglobin 18
Personal story: Mary — thalassaemia minor 19
Lipids 21
Nucleic acids 23
Biology in the workplace: Drew Berry — animator specialising in
biomedical science 27
Biochallenge 28
Key words 29
Questions 29
2 Membranes and cell organelles 32
Life or death for a cell? 33
Apoptosis 34
Biology in the workplace: Sue Macaulay — Chief Radiographer,
St Vincent’s BreastScreen 36
Looking at eukaryotic cells 37
Plants have cell walls 42
Putting the organelles together 51
The cell skeleton 52
Connections between cells: animal cells 52
Connections between cells: plant cells 54
Biochallenge 56
Key words 57
Questions 57
3 Biochemical processes in cells 60
Energy in a capsule? 61
Chemical energy in organic compounds 62
Enzyme action 64
Exploring photosynthesis 69
Which wavelengths of light are most useful? 70
Stages of photosynthesis 72
Comparing C3 and C4 plants 73
Plants — chemical factories 75
Putting photosynthesis together 75Cellular respiration: energy transfer from glucose to ATP 78Two types of cellular respiration 79ATP: Energy currency of cells 80Aerobic respiration: making ATP in the presence of oxygen 81
UNIT 3
Signatures of life
AREA OF STUDY 1Molecules of life
Energy needs of various tissues 85Biotech: The hyperbaric oxygen chamber 86PET images: assessing damage to heart muscle 87Making ATP without oxygen: anaerobic respiration 89Personal story: Kelly Stubbins — elite swimmer and student 90What happens during starvation? 93Elite athletes and their energy sources 94Biochallenge 96Key words 97
Questions 97
4 Molecular biology in medicine 100
Molecular biology — the beginning 101Inherited diseases 102Personal story: Joel Sheahan — living with PKU 105Gene therapy 106Medical diagnosis 109
Personal story: Angela — living with the possibility of Huntington disease 113Rational drug design 114Sir Ronald Ross — Nobel Laureate for his work on malaria 121Manufacturing biological molecules 123Biologist at work: Alister Ward — molecular research for
leukaemia 127Biochallenge 128Key words 129
Questions 129
5 Coordination and regulation:
endocrine systems 132Death at sea 133External and internal environments 134Homeostasis: keeping within limits 136Homeostasis: hormones in action 139
Personal story: Sophie’s story — my life with diabetes 142Biology in the workplace: Trisha Dunning — diabetes nurse
educator 143Cell communication 145Personal story: Maggy Saldais — adventures with
a hormone imbalance 149Pheromones 150Hormones as plant regulators 152Commercial uses of plant hormones 158Biochallenge 162Key words 163Questions 163
vi CONTENTS
UNIT 3
Signatures of life
AREA OF STUDY 2Detecting and
responding
6 Coordination and regulation:
nervous systems 166A bundle of nerves 167
Biology in the workplace: Claire Jackson — optometrist 169
The nervous system 170
Nerve cells 172
What is a nerve impulse? 174
Nerve cells communicate with other cells 175
Headache — is it a pain in the head? 182
The central nervous system 183
Looking into the brain with PET and CAT scans 186
Nerve action and hormone action: a comparison 187
Quick-change artists 188
Homeostasis: nerves and hormones acting together 189
Personal story: Patricia Hulskamp — kidney transplant
recipient 194
Biochallenge 196
Key words 197
Questions 197
7 Infection and disease 199
A plague of plagues 200
What is a disease? 203
Pathogens — non-cellular agents 204
Another non-cellular pathogen — viruses 207
Infl uenza — a common viral disease 210
An Australian Nobel Laureate — Sir Macfarlane Burnet
(1899–1985) 212
Pathogens — cellular agents: bacteria 213
Mary Mallon — a famous carrier of typhoid 219
Lethal sandwiches 220
Treatment of bacterial diseases 221
Penicillin — the miracle drug 222
New techniques for detecting bacteria 223
Bacteria and plant infections 224
Biology in the workplace: Cathy Harcourt —
medical laboratory scientist 225
Eukaryotic pathogens 226
Multi-celled organisms 227
Sexually transmitted diseases 233
Control against pathogens 235
Biologist at work: Dr Anneke Veenstra-Quah —
animal biologist 238
Biochallenge 240
Key words 241
Questions 241
CONTENTS vii
8 Immunity: defence against disease 244
A vaccine for cervical cancer 245
Immunity 246
Non-specifi c immunity 246
Specifi c immunity 250
Colony stimulating factors — csfs 252
The Walter and Eliza Hall Institute of Medical Research 260
Acquiring specifi c immunity 263
Eradicating a disease by vaccination 265
Adverse events associated with immunity 269
Trent — allergic to peanuts and dairy products 270
Personal story: Rachel’s story — a case of systemic lupus
erythematosus (sle) 276
Biochallenge 280
Key words 281
Questions 281
9 Genes, chromosomes and patterns of
inheritance 286The genetic lottery 287
Biologist at work: Lisette Curnow — genetic counsellor 290
Chromosomes: gene carriers 291
Personal story: Jane’s story, as told by her mother 298
Meiosis: diploid to haploid 302
Genes: inherited instructions 306
Alleles: particular forms of a gene 309
Identifying genotypes 312
Relationship between expression of alleles 314
Tortoiseshell cats and the X chromosome 315
Environmental interactions with genotypes 318
Rules of the genetic game 321
What about linked genes? 324
Estimating distance between linked genes 326
Family pedigrees: drawing genetic portraits 328
Biology in the workplace: Associate Professor Jane Halliday
— epidemiologist 332
Biochallenge 334
Key words 335
Questions 335
10 Nature, structure and organisation of the
genetic material 339In a monastery garden 340
Where are genes located? 346
What are genes made of? 348
Nature of genes 351
Analysing DNA 351
DNA forms a double helix 353
Relating DNA to chromosomes and genes 356
viii CONTENTS
UNIT 4
Continuity and change
AREA OF STUDY 1Heredity
Gene structure 358
Gene sequencing 359
DNA sequencers 360
Nature of the genetic code 362
What is a genome? 365
Biologist at work: Dr Sue Forrest — molecular geneticist 369
Genetic material: stable or changing? 370
A closer look at a gene 373
A royal mutation 374
Coding and fl anking regions 375
Finding the double helix 377
Biochallenge 379
Key words 380
Questions 380
11 Gene function: genes in action 384
Sea in the blood 385
Personal story: Soltirios — living with thalassaemia 387
Genes in action 388
Transcription: copying the original 389
Translation: decoding genetic instructions 391
Comparing prokaryotes and eukaryotes 395
Gene action in thalassaemia 397
‘Beta plus’ — another form of thalassaemia 399
All genes produce RNA . . . most then produce protein 400
Genes have various functions 401
Self-replication: copying itself 403
A closer look at DNA replication 405
Time and place for everything 406
Gene action in Mendel’s peas 407
How do microarrays work? 409
Switching genes off 409
How does RNA interference work? 410
Biochallenge 413
Key words 414
Questions 414
12 Manipulating DNA: tools and techniques 418
Murders at Ekaterinberg 419
Tools of the genetic engineer 422
Eco RI — what’s in a name? 422
Getting hold of specifi c DNA 427
Making multiple copies of a gene 428
Amplifying traces of DNA 429
Gene transfer between species 431
DNA technology in medicine 433
Protocol for predictive testing for HD 436
DNA technology in forensics 437
DNA profi ling in Australia 443
What’s my DNA profi le? 446
CONTENTS ix
DNA profi les are not just for people! 448
Biologist at work: Peter Timms — DNA wildlife detective 450
Identifi cation in mass disasters 455
DNA and paternity testing 455
Biologist at work: Linzi Wilson-Wilde OAM — forensic
scientist 456
Biochallenge 458
Key words 459
Questions 459
13 Population genetics 464How now, red fowl! 465
Causes of variation 471
Inherited variations 474
Polygenes in action 476
Mutation: source of new genetic variation 477
Biotech: Visualising genetic variation in a population 478
Genes in populations 479
Math in biology: Hardy–Weinberg in action 481
Change agents in populations 483
Migration as an agent of change 490
Chance as an agent of change 491
Evolution within a species 492
Biologists at work: David Westcott and Peter Latch —
wild populations 493
Studying populations using mtDNA 494
Biochallenge 499
Key words 500
Questions 500
14 Evolution: changes over time 505Evolution: history of ideas 506
The Darwin–Wallace view 508
The Oxford debate of 1860 510
The travels of Darwin and Wallace 516
Time scales in evolution 517
Organising the past: the geologic time scale 519
How old is it? 520
Evidence of evolution 525
The ‘molecular clock’ concept 544
Patterns of evolution 546
Speciation 553
Evolution: gradual or intermittent? 553
Extinction 554
Evolutionary relationships 555
Biochallenge 559
Key words 560
Questions 560
UNIT 4
Continuity and change
AREA OF STUDY 2Change over time
x CONTENTS
15 Hominin evolution 565
Fossil 1: The child from Taung 566
Fossil 2: Lucy from Afar 569
Classifi cation of the human species 572
Classifi cations can change 577
Evolution of the primates 579
Hominin evolution: where did it begin? 581
Ancestral players in human evolution 585
The genus Homo: human at last! 591
Geologist at work: Professor Ian McDougall 594
Views of human evolution 602
Out of Africa or not? 604
Changing lifestyles of H. sapiens 605
Changes in human population 607
Human biological evolution 607
Human cultural evolution 611
Technological evolution 613
Biology, culture and technology interact 614
Developments in tool making 614
Meet a fossil hunter: Sue Hand — Palaeontologist 616
Biochallenge 617
Key words 618
Questions 618
16 Human intervention in evolution 620
Lambs in spring 621
Selective breeding in action 622
Reproductive technologies 624
No sex at all! Cloning 629
Transferring genes between species 636
Is it a GMO or a TGO or both? 637
Gene therapy 639
Cystic fi brosis and gene therapy 640
Stem cells: a new approach 640
Genetic screening 644
Technology in human reproduction 645
Biotech: Assisting reproduction in humans 648
Biotech: Reducing the chance of implanting
a defective embryo 649
Personal story: Maggie Kirkman — parenthood through biology,
technology and generosity 650
Biochallenge 652
Key words 653
Questions 653
Appendix 656
Glossary 657
Index 674
CONTENTS xi
PREFACE
This third edition of Nature of Biology Book 2 builds on previous editions that were positively received by
teachers and students of biology. It has been thoroughly revised and updated and refl ects current curriculum decisions with regard to key knowledge and skills expected of biology students.
This book continues to seek to convey a multifaceted sense of biology: as a rigorous scientifi c discipline with explanatory models that organise the living world for us in a meaningful way; as a dynamic science whose explanations are subject to change, rather than as a fi xed and unchanging body of knowledge; as a science that impacts on everyday life, at the level of the individual where it can inform personal choices and at a societal level where it can inform community and government decisions.
The domain of biology does not stand still and new technologies provide additional insight to our understanding of this science. In the third edition of Nature
of Biology Book 2, we have included new topics that refl ect both the changing curriculum and advances in knowledge. These additions include:
• transduction, the process by which cellular messages are translated into action
• expanded details of apoptosis, the programmed death of a cell, which can be initiated from inside or outside a cell
• details regarding the role of Australian scientists in a range of developments, such as rational drug design, new ways of preparing and delivering vaccines, and new vaccines, including one against the papilloma virus that may reduce the incidence of cervical cancer by 90 per cent
• new hominin fossil species discoveries such as that of Homo fl oresiensis, an announcement that excited the world in October 2004
• latest data, announced in February 2005, on the age of the oldest well-dated fossils of modern humans.
In the molecular and technological domains, additions include comparative genomics; microarray technology, which can identify active genes; RNA interference (RNAi), which enables genes to be selectively switched off; DNA profi ling and databases; and stem cell technology.
In this book, we have used the latest classifi cation of the human species that uses the term ‘hominin’ rather than ‘hominid’ to describe humans and their extinct, erect-walking relatives. We have also chosen to remove the peppered moth as an example of a well-understood case of natural selection in action with bird predation as the agent of selection. Because bird predation is apparently not the sole agent of selection, we have used other examples, although change in peppered moth populations is still an undisputed case of evolution within a species.
We have enjoyed writing this book and we hope that our readers will also enjoy reading the text and exploring the visual images. This project was greatly enhanced by the generous cooperation of many colleagues, friends and acquaintances. In particular, we owe a special debt of
gratitude to the following:
Professor Suzanne Cory, Director, and Dr Margaret Brumby, Manager (Walter and Eliza Hall Institute of Medical Research), Associate Professor Leigh Ackland (Deakin University), Dr Michael Ackland (Public Health Division, Department of Health Services), Rachel Altemus (Editorial Offi ce, Molecular
Biology of the Cell), Jamie Alvarez (USA), Margaret Anderson, Professor Mike Archer (UNSW), Dr Peter Beech (Deakin University), Sarah Bell (Andrew Gaddes Optometrists Pty Ltd), Suzanne Bennett (Burnet Institute), Drew Berry (Walter and Eliza Hall Institute of Medical Research), Mauro Bolin, Nicole Bolin (President, Chromosomal Labs, USA), Joanne Broughton (Invitrogen), Dr Lynda Campbell (St Vincent’s Hospital), Terry Carmichael (GeneTree DNA Testing Center), Gillian Chamberlain (Burnet Institute), Paul Charteris (MMI Genomics Inc.), Mary Cotronis, Dr Jenny Cox (University of Sydney), Lisa Curnow (Murdoch Childrens Research Institute), Hilary Taylor Deayton, Dr Martin Delatycki (Murdoch Childrens Research Institute), Eddie Dixon (Premier Genetics NZ Ltd), Professor Trisha Dunning (St Vincent’s Hospital and The University of Melbourne), Dr Sue Forrest (Australian Genome Research Facility), Joyce Francis, Doug Gale (CSIRO Molecular Science), Christine A. Gigliotti (Applied Biosystems), Associate Professor Dawn Gleeson (The University of Melbourne), Professor Sue Hand (UNSW), Cathy Harcourt (Alexandra District Hospital), Jethro Harcourt, Harcourt family, Dr Jane Halliday (Murdoch Childrens Research Institute), Katrina Harrison (Biota Holdings Limited), Anders and Maj Britt Hedlund (Sweden), Drs Jane and Gene Heinz-Fry, John and Tania Hulskamp, Professor Jeremy Hyams (Massey University), Claire Jackson (Andrew Gaddes Optometrists Pty Ltd), Clem Kandiliotis, Sandra Kay (CSIRO Tropical Forest Research Centre), Dr Josephine Kenrick (The University of Melbourne), Dr Maggie Kirkman and family, Dr Silvia M Kreda (MH Microscopy Facility, The University of North Carolina at Chapel Hill), Professor David Lambert (Massey University), Rachel Lea, Jean-Marc Lefebvre-Despeaux (BLUESTAR Forensic), Ruth Leslie (Chisholm Institute of TAFE), Sue Macauley (St Vincent’s BreastScreen), Dr John G Mason (Manager R&D, Florigene Ltd), Jane McCooey (La Trobe University), Dr Ian McDougall (ANU), Dr Brian McStay (Biomedical Research Centre, University of Dundee), Dr Marilyn Menotti-Raymond (National Cancer Institute, MD, USA), Professor Julian Mercer (Deakin University), Dr Agnes Michalczyk (Deakin University), Margaret Perring, Julia Quince (Massey University), Dr Tariq M. Rana (Professor and Director of Chemical Biology Program, University of Massachusetts Medical School), Mary and Jane Rice, Dr Hugh Robinson (Monash Medical Centre), Professor Al Rowland (Massey University), Maggy Saldais, M. Suzanne Searls, Elaine and Michael Sewell, Mardi and Joel Sheahan, Kerrie Simonsen (Massey University), Dr George Sofronidis (Animal Diagnostics, Genetic Science Services), Soltirios, Sophie Stone, Peta Stringer (Victoria Police Forensic Services Centre), Kelly Stubbins, Dallis Sturtevant, Ros Tassiker (Murdoch Childrens Resarch Institute), Professor Peter Timms (Queensland University of Technology), Dr Anneke Veenstra-Quah (Deakin University), Verity family, Associate Professor Alister Ward (Deakin University), Fiona and Trent Wedding, Dr David Westcott (CSIRO Tropical Forest Research Centre), Christopher Wilson (Monash University), Linzi Wilson-Wilde (Coordinator Laboratory Services, Forensic Services, AFP), David Wiltshire (Massey University).
xii PREFACE
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ABOUT THE CD-ROM xiii
CROSSWORD
ACKNOWLEDGEMENTS
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xiv ACKNOWLEDGEMENTS
ACKNOWLEDGEMENTS
Kinnear and Marjory Martin; 514 (left)/Journal of Researches (now known as Voyage of the Beagle) 1840 • © Lawrence Berkeley National Laboratory: 21 • Rachel Lea: 276, 277 • © Lochman Transparencies: 551 (top)/Andrew Davoll; 486/Hans & Judy Beste • Sue Macaulay: 36 • Adapted by permission from Macmillan Publishers Ltd: Nature/Comparative analyses of multi-species sequences from targeted genomic regions, © 2003: 556 • MAPgraphics Pty Ltd Brisbane: 118 (top), 210 (bottom), 237 (2 maps), 502 (2 maps), 512 (right), 516, 561 (bottom), 605 • Marjory Martin: 5 (right), 9, 12 (top), 13 (top left, bottom), 19, 28 (Q1), 37, 61 (top), 70, 77 (2 images), 98, 127 (2 images), 151 (left), 169, 187 (2 images), 201 (bottom), 203, 210 (top), 214 (4 images), 216, 222 (2 images), 223, 225, 229, 265, 270, 279, 288 (top right), 293 (2 images), 296 (2 images), 310, 374, 384 (4 corn images), 404, 416, 436, 526 (bottom right), 650; 332/Courtesy of Jane Halliday; 497 (cartoon)/Courtesy of Jethro Harcourt; 289 (top)/Courtesy of the authors and Margaret Perring; 298/Jane Rice/C- Marjory Martin; 305, 310–11, 311 (4 images), 317, 334, 315 (2 images), 319 (bottom), 386, 435 (2 images)/Judith Kinnear and Marjory Martin; 5 (left)/Maj-Britt and Anders Hedlund; 434/Marjory Martin and Judith Kinnear; 330/Simon; 372 (left)/The authors/Dr Gillian Tucker; 372 (centre, right)/The authors/Dr Graham Webb; 387/The authors/Thalassaemia Society • Courtesy Professor Ian McDougall: 594 • Courtesy Dr Brian McStay, Biomedical Research Centre, University of Dundee: 401 • Courtesy of Dr Marilyn Menotti-Raymond, National Cancer Institute, Frederick MD: 451 (2 images) • Courtesy NASA/JPL–Caltech: 554 • Reproduced from ‘Human neural stem cells differentiate and promote locomotor recovery in spinal cord-injured mice’ by Brian J. Cummings, Nobuko Uchida, Stanley J. Tamaki, Desiree L. Salazar, Mitra Hooshman, Robert Summers, Fred H. Gage and Ailenn J. Anderson, in PNAS vol. 102, issue 39, September 27, 2005, © 2005 National Academy of Sciences, U.S.A. Image by Robert Summers: 641 (top) • Courtesy: National Human Genome Research Institute: 368 (top), 394 • D.C Johnson, Institute of Human Origins, Courtesy of National Museum of Ethiopia: 569 • National Portrait Gallery, London: 510 (right), 512 • Newspix: 199; 633 (lower right 2 images)/AFP/Nature Magazine; 633 (top left)/Chris Crerar; 86/Colleen Petch; 369/Jon Hargest; 122/Kelly Barnes; 601 (lower)/Michael Jones; 446 (bottom)/Michael Marschall; 245 (bottom)/Patrick Hamilton; 428 (left)/Russell Millard • Nuclear Medicine, Royal Prince Alfred Hospital, Sydney: 88, 186 (left) • Courtesy Nutricia Australia Pty Ltd: 103 (2 images) • © Ivan Ovcharenko, Ph.D.: 557 • Adapted from p. 19 of The Viking Atlas of Evolution by Roger Osbourne and Michael Benton (Viking 1996) text © Roger Osbourne and Michael Benton, 1996. Design © Swanston Publishing Ltd, 1996: 548 • PhotoDisc, Inc.: 92 (right), 131, 219, 285, 373, 463, 573 (ape, baboons, man and child, white loris), 575 (2 images), 597 (right), 601 (radiation, yin yang), 608, 614
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(2 images) • Courtesy Dr Mariano Rocchi: 538 • Courtesy of the Rockefeller University Archives: 350 (top) • © The Roslin Institute: 631 (2 images) • Courtesy of Dr A.l. Rowland: 294 (top) • By permission of the Royal Mint: 23 (right) • Joel Sheahan: 105 (3 images) • Courtesy of George Sofronidis, Genetic Science Services: 452 (top, bottom), 453 (2 images), 458 • G. & R. Small of Abrona Suffolks and White Suffolks: 622 (right) • Courtesy Dr Arabella Smith, The Children’s Hospital at Westmead: 319 (top), 336, 425 • © Sport The Library/Paul Seiser: 91 • Stock Journal/Rural Press Limited: 627 • Nikki Stubbins: 90 • Courtesy Sydney IVF, www.sydneyivf.com.au: 359 (bottom), 420 • John Thomas, Queensland Government, Department of Primary Industries and Fisheries: 211
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bottom right), 263, 273, 284 (2 images), 289 (bottom left, bottom right), 413, 478, 641 (centre, bottom) • Dr David Westcott (CSIRO) and Peter Latch (QPWS): 493 • Courtesy of Linzi Wilson-Wilde: 456 • Courtesy Zoological Society of San Diego: 288 (top left)
Text
• Reprinted with permission from Journal of Forensic
Sciences, vol. 49, no. 5, © ASTM International, 100 Barr Harbour Drive, West Conshohocken, PA 19428: 442 • Immunise Australia Program, Department of Health and Ageing, 2005, © Commonwealth of Australia. Reproduced by permission. By permission also from the Immunisation Program, Department of Human Services Victoria: 268 • The Double Helix by James Watson, published by Weidenfeld & Nicolson, an imprint of The Orion Publishing Group. Reproduced with permission: 377–8
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xvi ACKNOWLEDGEMENTS