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OXFORD IB STUDY GUIDES Andrew Allott Biology F O R T H E I B D I P LO M A 2014 edition 2 3 Great Clarendon Street, Oxford, OX2 6DP, United Kingdom Oxford University Press is a department of th...
OXFORD IB STUDY GUIDES Andrew Allott Biology F O R T H E I B D I P LO M A 2014 edition 2 3 Great Clarendon Street, Oxford, OX2 6DP, United Kingdom Oxford University Press is a department of the University of Oxford. It furthers the Universitys objective of excellence in research, scholarship, and education by publishing worldwide. Oxford is a registered trade mark of Oxford University Press in the UK and in certain other countries Oxford University Press 201 4 The moral rights of the authors have been asserted First published in 201 4 All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, without the prior permission in writing of Oxford University Press, or as expressly permitted by law, by licence or under terms agreed with the appropriate reprographics rights organization. Enquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, at the address above. You must not circulate this work in any other form and you must impose this same condition on any acquirer British Library Cataloguing in Publication Data Data available 978-0-1 9-839351 -1 10 9 8 7 6 5 4 3 2 1 Paper used in the production of this book is a natural, recyclable product made from wood grown in sustainable forests. The manufacturing process conforms to the environmental regulations of the country of origin. Printed in Great Britain Acknowledgements The publishers would like to thank the following for permissions to use their photographs: Artwork by OUP and Six Red Marbles Cover image: Martin Harvey / Alamy p1: http://www.ncbi. 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Interested PHOTO LIBRARY; p4: Michael Abbey/SCIENCE PHOTO LIBRARY; parties should apply to the copyright holders indicated in each p5: OUP; p5: The American Association for the Advancement case. of Science; p5: OUP; p5: OUP; p5: THOMAS DEERINCK, NCMIR/ SCIENCE PHOTO LIBRARY; p6: MOREDUN ANIMAL HEALTH LTD/SCIENCE PHOTO LIBRARY; p6: OUP; p6: Jmol; p6: Jmol; p6: Jmol; p6: Public Domain; p6: OUP; p6: http://www3. nd.edu; p6: Dr. Michal Laurent, KULeuven, Belgium; p7: OUP; p8: OUP; p8: OUP; p8: Public Domain; p8: Dr. Gladden Willis/ Getty Images; p8: Image Source/Getty Images; p9: OUP; p9: OUP; p9: OUP; p9: Public Domain; p10: MEDICAL SCHOOL, UNIVERSITY OF NEWCASTLE UPON TYNE/SIMON FRASER/ Introduction and acknowledgements th IB Biy P h b phivy vi i y vp hiq i bfi y, b hi spb 2014 . thi b h b h h h h i i p h i vi i i ii y. a hh i h piip hp f h ii h hy qiy biy i i i h h iy h yi h p. h h ppii. Biy h a pi i Hih lv (Hl) s lv (sl) Biy i h i b h v, ii pi. th pi v i hy i pi hi i. th IB h q i h yb, b ihi pi Biy ii h p h q b-pi h b ihy , iv ii i. th y ppii h pi i. hi i Biy. ap h, ivi i iz i i. livi i hh tpi 16 pi i bh Hl sl. h biph, ii h, ip. tpi 711 ii pi i y Hl. H ivii hv ii ip, ii opi ad b i Hl sl, ih x i pi i i p h biph i Hl, p y p h -h biiviy. h pi. P h h p, y I vy h hp h h hv iv pi i i. i h ii hi b. e w ox Pi qi i h pi pi. uiviy P hp, Ji th a h qi iv, hh i hi py i. I ib y i ai h y b b f h vi ! wii hi pp b i h gi i iv i i y h h I hv p i. I i i ppi f x. h h I i h b bii h , h ivi v ivi i th h v b ip xii i hi hbi. y biy. th p ppii I n tr o d u c tI o n an d ac kn o wle d g e m e n ts iii Contents 1 cell BIologY Autosomal genetic diseases 43 Cell theory 1 Sex-linkage 44 Unicellular and multicellular organisms 2 Co-dominance 45 Stem cells 3 Mutation 46 Light microscopes and drawing skills 4 Genes and alleles 47 Electron microscopes and ultrastructure 5 Gene sequencing 48 Prokaryotic cells 6 DNA technology 49 Eukaryotic cells 7 DNA proling 50 Models o membrane structure 8 Genetic modication 51 Membrane structure 9 Cloning 52 Diusion and acilitated diusion 10 Questions genetics 53 Osmosis 11 4 ecologY Active transport 12 Modes o nutrition 54 Origins o cells 13 Communities and ecosystems 55 Mitosis 14 Energy fow 56 Cell cycles and cancer 15 Food chains and energy pyramids 57 Questions cell biology 16 Nutrient cycles 58 2 molecular BIologY Carbon cycle 59 Molecules to metabolism 17 Global warming and the greenhouse eect 60 Water 18 Rising carbon dioxide concentrations 61 Water and lie 19 Questions ecology 62 Carbohydrates 20 5 eVolutIon and BIodIVersItY Molecular visualization o polysaccharides 21 Introducing evolution 63 Lipids 22 Further evidence or evolution 64 Lipids and health 23 Natural selection 65 Amino acids and polypeptides 24 Natural selection in action 66 Protein structure and unction 25 Naming and identiying 67 Enzymes 26 Classication o biodiversity 68 Factors aecting enzyme activity 27 Classication o eukaryotes 69 Structure o DNA and RNA 28 Cladistics 70 DNA replication 29 Questions evolution and biodiversity 71 Transcription and translation 30 6 Human PHYsIologY The genetic code 31 Digestion 72 Cell respiration 32 Absorption 73 Respirometers 33 The cardiovascular system 74 Photosynthesis 34 The heart 75 Investigating limiting actors 35 Deence against inectious disease 76 Chromatography 36 Antibodies and antibiotics 77 Questions molecular biology 37 Ventilation 78 3 genetIcs Gas exchange 79 Chromosomes 38 Neurons and synapses 80 Karyograms 39 Nerve impulses 81 Meiosis 40 Regulating blood glucose and body temperature 82 Meiosis and genetic variation 41 Leptin and melatonin 83 Principles o inheritance 42 Reproductive systems 84 iv co n te n ts Conception and pregnancy 85 Chi-squared and continuous variation 126 Research into reproduction 86 Speciation 127 Questions human physiology 87 Questions genetics and evolution 128 7 nucleIc acIds 11 anImal PHYsIologY Landmarks in DNA research 88 Antigens and allergy 129 DNA replication 89 Antibody production 130 Base sequences in DNA 90 Vaccination and monoclonal antibodies 131 Bioinormatics and nucleosomes 91 Muscle 132 Gene expression 92 Muscle contraction 133 Epigenetics 93 Movement 134 Ribosomes and transer RNA 94 Excretion and osmoregulation 135 Translation 95 Kidney structure and ultraltration 136 Primary and secondary structure o proteins 96 Urine production and osmoregulation 137 Tertiary and quaternary structure o proteins 97 Kidney unction and kidney ailure 138 Questions nucleic acids 98 Excretion and osmoregulation in animals 139 8 metaBolIsm, cell resPIratIon Spermatogenesis 140 Oogenesis 141 and PHotosYntHesIs Fertilization 142 Enzymes and activation energy 99 Pregnancy and childbirth 143 Enzyme inhibition 100 Structure and unction o the placenta 144 Controlling metabolic pathways 101 Questions animal physiology 145 Glycolysis 102 Krebs cycle 103 a neuroBIologY and BeHaVIour ATP production by oxidative phosphorylation 104 Neurulation 146 Mitochondria 105 Development o the nervous system 147 Light-dependent reactions o photosynthesis 106 Functions o the brain 148 Chloroplast structure 107 Cerebral hemispheres 149 Light-independent reactions o photosynthesis 108 Perception o stimuli 150 Calvins experiments 109 Vision in humans 151 Questions metabolism, cell respiration and Hearing in humans 152 photosynthesis 110 Innate behaviour (HL only) 153 9 Plant BIologY Learned behaviour (HL) 154 Transpiration 111 Neurotransmitters and synapses ( HL only) 155 Investigating transpiration 112 Ethology (HL only) 156 Water uptake and water conservation 113 Questions neurobiology and behaviour 157 Vascular tissue in plants 114 B BIotecHnologY and InFormatIcs Water transport in xylem 115 Microorganisms and ermenters 158 Phloem transport 116 Microorganisms in industry 159 Research in plant physiology 117 Genetic modication o crop plants 160 Plant hormones and growth o the shoot 118 Bioremediation 161 Reproduction in fowering plants 119 Biotechnology in diagnosis ( HL only) 162 Propagating plants 120 Biotechnology in therapy (HL only) 163 Questions plant biology 121 Bioinormatics (HL only) 164 10 genetIcs and eVolutIon Questions biotechnology and bioinormatics 165 Mendels law o independent assortment 122 c ecologY and conserVatIon Dihybrid crosses 123 Community structure 166 Genes linked and unlinked 124 Interactions and energy fow 167 Crossing-over 125 Nutrient cycles and change in ecosystems 168 c o n te n ts v Impacts o humans on ecosstems 169 Cardiolog 179 Biodiversit and conservation 170 Endocrine glands and hormones (HL onl) 180 Populations ( HL onl) 171 Carbon dioide transport (HL onl) 181 Nitrogen and phosphorus ccles (HL onl) 172 Ogen transport (HL onl) 182 Questions ecolog and conservation 173 Questions human phsiolog 183 d Human PHYsIologY Human nutrition 174 ExAM ADVICE 184 Defcienc diseases and diseases o the gut 175 NATURE OF SCIENCE A SUMMARy 186 Digestion and absorption 176 ADVICE FOR INTERNAL ASSESSMENT (IA) 188 Liver 177 ANSWERS TO QUESTIONS 189 Cardiac ccle 178 INDEx 196 vi co n te n ts 1 CE LL B I O LO G Y Cell theory INTRODUCING THE CELL THEORY One the most important theories in biology is that cells are the o indivisible subunits, but the invention o the microscope smallest possible units o lie and that living organisms are settled this debate. Cells consist o cytoplasm, enclosed in a made o cells. The ancient Greeks had debated whether living plasma membrane. In plant and animal cells there is usually a organisms were composed o an endlessly divisible uid or nucleus that contains genes. Human cheek cell Moss leaf cell cytoplasm chloroplasts plasma membrane cell wall nucleus plasma cytoplasm membrane nucleus mitochondria sap in vacuole vacuole membrane EXCEPTIONS TO THE CELL THEORY DRAWINGS IN BIOLOGY The cell theory was developed because biologists observed The command term draw is defned by IB as: Represent a trend or living organisms to be composed o cells. Scientifc by means of a labelled, accurate diagram or graph, using theories can be tested by looking or discrepancies cases a pencil. A ruler (straight edge) should be used for straight that do not ft the theory. There are some tissues and lines. Diagrams should be drawn to scale. organisms that are not made o typical cells: A sharp pencil with a hard lead (2H) should be used. This allows 1. Skeletal muscle is made up o muscle fbres. Like cells clear, sharp single lines to be drawn. In exams, diagrams should these fbres are enclosed inside a membrane, but they not be drawn aintly as they will not show clearly in scans. are much larger than most cells (300 or more mm long) and contain hundreds o nuclei. 2. Giant algae such as Acetabularia (below) can grow to a length o as much as 100mm so we would expect them to consist o many small cells but they only contain a single nucleus so are not multicellular. bad good There should be no gaps, overlaps or multiple lines. cytoplasm bad good Labelling can be in ink or pencil, with labelling lines rather 20 mm than arrows. Labelling lines should be drawn using a ruler and they should point precisely to the structure being labelled. nucleus 3. Aseptate fungi consist o thread-like structures called hyphae. These hyphae are not divided up into sub-units containing a single nucleus. Instead there are long undivided sections o hypha which contain many nuclei. cell cell Despite these and some other discrepancies, there is still a bad good strong overall trend or living organisms to be composed o cells, so the cell theory has not been abandoned. C E LL B I O LO G Y 1 Unicellular and multicellular organisms FUNCTIONS OF LIFE IN UNICELLULAR ORGANISMS Unicellular organisms consist o only one cell. They carry out all unctions o cilia lie in that cell. Two examples are given agellum here: Paramecium lives in ponds and contractile vacuole is between a twentieth and a third o a eye spot millimetre long. Chlamydomonas lives in plasma membrane reshwater habitats and is between 0.002 nucleus cell wall and 0.010 millimetres in diameter. They cytoplasm chloroplast are similar in how they carry out some unctions o lie and dierent in others. food in vesicles Paramecium Chlamydomonas Function Paramecium Chlamydomonas Nutrition Feeds on smaller organisms by ingesting and Produces its own ood by photosynthesis using a digesting them in vesicles (endocytosis) chloroplast that occupies much o the cell Growth Increases in size and dry mass by accumulating Increases in size and dry mass due to organic matter and minerals rom its ood photosynthesis and absorption o minerals Response Reacts to stimuli, e.g. reverses its direction o Reacts to stimuli, e.g. senses where the brightest movement when it touches a solid object light is with its eyespot and swims towards it Excretion Expels waste products o metabolism, e.g. CO 2 Expels waste products o metabolism, e.g. oxygen rom respiration difuses out o the cell rom photosynthesis difuses out o the cell Metabolism Both: produces enzymes which catalyse many diferent chemical reactions in the cytoplasm Homeostasis Both: keeps internal conditions within limits, e.g. expels excess water using contractile vacuoles Reproduction Both: reproduces asexually using mitosis or sexually using meiosis and gametes MULTICELLULAR ORGANISMS DIFFERENTIATION As a cell grows larger its surace area to volume ratio An organisms entire set o genes is its genome. In a becomes smaller. The rate at which materials enter or leave multicellular organism each cell has the ull genome, so it a cell depends on the surace area o the cell. However, the has the instructions to develop into any type o cell. During rate at which materials are used or produced depends on the diferentiation a cell uses only the genes that it needs to ollow volume. A cell that becomes too large may not be able to take its pathway o development. Other genes are unused. For in essential materials or excrete waste substances quickly example, the genes or making hemoglobin are only expressed enough. Large organisms are thereore multicellular they in developing red blood cells. Once a pathway o development consist o many cells. has begun in a cell, it is usually xed and the cell cannot change Being multicellular has another advantage. It allows to a diferent pathway. The cell is said to be committed. division o labour diferent groups o cells (tissues) become specialized or diferent unctions by the process Heart muscle tissue 20 m o diferentiation. The drawings (right) show two o the hundreds o types o diferentiated cell in humans. EMERGENT PROPERTIES Emergent properties arise rom the interaction o the Pancreatic islet cell component parts o a complex structure. We sometimes sum this up with the phrase: the whole is greater than the sum o its parts. Multicellular organisms have properties that emerge rom the interaction o their cellular components. For example, each cell in a tiger is a unit o lie that has distinctive properties such as sensitivity to light in retina cells, but all o a tigers cells combined give additional emergent properties or example the tiger can hunt and kill 4000 and have a proound ecological efect on its ecosystem. vesicles of insulin 2 C E LL B I O LO G Y Stem cells STEM CELLS ETHICS OF THERAPEUTIC USE OF Stem cells are dened as cells that have the capacity to divide STEM CELLS and to diferentiate along diferent pathways. Human embryos Ethics are moral principles that allow us to decide consist entirely o stem cells in their early stages, but gradually whether something is morally right or wrong. Scientists the cells in the embryo commit themselves to a pattern o should always consider the ethics o research and its diferentiation. Once committed, a cell may still divide several consequences beore doing it. more times, but all o the cells ormed will diferentiate in the same way and so they are no longer stem cells. The main argument in avour o therapeutic use o stem cells is that the health and quality o lie o patients sufering rom Small numbers o cells persist as stem cells and are still otherwise incurable conditions may be greatly improved. present in the adult body. They are ound in most human Ethical arguments against stem cell therapies depend on the tissues, including bone marrow, skin and liver. They give source o the stem cells. There are ew objections to the use some human tissues considerable powers o regeneration o an adults own stem cells or cells rom an adult volunteer. and repair, though they do not have as great a capacity to Newborn babies cannot give inormed consent or stem cells to diferentiate in diferent ways as embryonic stem cells. be harvested rom their umbilical cord, but parental consent is Other tissues lack the stem cells needed or efective given and the cells are stored in case they are needed during repair brain, kidney and heart, or example. There has the babys subsequent lie, which seems unobjectionable. been great interest in the therapeutic use o embryonic stem However, the ethical issues concerning stem cells taken rom cells with organs such as these. There is great potential or specially created embryos are more controversial. Some argue the use o embryonic stem cells or tissue repair and or that an embryo is a human lie even at the earliest stage and treating a variety o degenerative conditions, or example i the embryo dies as a result o the procedure it is immoral, Parkinsons disease. because a lie has been ended and benets rom therapies using embryonic stem cells do not justiy the taking o a lie. There are a several counter-arguments: early stage embryos are little more than balls of cells that have yet to develop the essential eatures o a human lie early stage embryos lack a nervous system so do not feel pain or sufer in other ways during stem cell procedures if embryos are produced deliberately, no individual that would otherwise have had the chance o living is denied the chance o lie large numbers of embryos produced by IVF are never implanted and do not get the chance o lie; rather than kill these embryos it is better to use stem cells rom them Removing a stem cell rom an embryo to treat diseases and save lives. EXAMPLES OF THERAPEUTIC STEM CELL USE 1. Stargardts macular dystrophy is a genetic disease that 2. Leukemia is a type o cancer in which abnormally develops in children between the ages o 6 and 12. Most large numbers o white blood cells are produced in the cases are due to a recessive mutation o a gene called bone marrow. A normal adult white blood cell count ABCA4. This causes a membrane protein used or active is 4,00011,000 per mm 3 o blood. With leukemia the transport in retina cells to malunction, so photoreceptive count rises above 30,000 and with acute leukemia above cells degenerate and vision becomes progressively worse. 100,000 per mm 3. The loss o vision can be severe enough or the person to Adult stem cells are used in the treatment o leukemia: be registered as blind. A large needle is inserted into a large bone, usually the Researchers have developed methods or making pelvis and uid is removed rom the bone marrow. embryonic stem cells develop into retina cells. This was Stem cells are extracted rom this uid and are stored by done initially with mouse cells but, in 2010, a woman in reezing them. They are adult stem cells and only have the her 50s with Stargardts disease was treated by having potential or producing blood cells. 50,000 retina cells derived rom embryonic stem cells injected into her eyes. The cells attached to the retina A high dose o chemotherapy drugs is given to the patient, and remained there during the our-month trial. There was to kill all the cancer cells in the bone marrow. The bone an improvement in the womans vision, and no harmul marrow loses its ability to produce blood cells. side efects. Further trials with larger numbers o patients The stem cells are then returned to the patients body. They are needed, but ater these initial trials at least, we can re-establish themselves in the bone marrow, multiply and be optimistic about the development o treatments or start to produce red and white blood cells. In many cases Stargardts disease using embryonic stem cells. this procedure cures the leukemia completely. C E LL B I O LO G Y 3 Light microscopes and drawing skills USING LIGHT MICROSCOPES MAGNIFICATION CALCULATIONS 1. Treat the specimen with a stain that makes parts o the Microscopes are used to investigate the structure o cells and cells o the specimen visible. tissues. Most microscopes use light to orm an image and can 2. Mount the specimen on a microscope slide with a cover make structures appear up to 400 times larger than their actual slip to make it at and protect the microscope. size. Electron microscopes give much higher magnications. 3. Put the microscope slide on the stage so the specimen is The structures seen with a microscope can be recorded below the objective lens. with a neat drawing or a photograph can be taken down the microscope called a micrograph. An important skill 4. Plug in the microscope and switch on the power so that in biology is calculating the magnication o a drawing or light passes through the specimen. micrograph. Use these instructions: 5. Focus with the low power objective lens rst. 1. Choose an obvious length, or example the maximum 6. Use the ocusing knobs to bring the slide and objective diameter o a cell. Measure it on the drawing. lens as close as possible without touching. 2. Measure the same length on the actual specimen. 7. Look through the eyepiece lens and move the slide and 3. I the units used or the two measurements are diferent, objective lens apart with the coarse ocusing knob until convert them into the same units. the specimen comes into ocus. One millimetre (mm) = 1,000 micrometres (m) 8. Use the ne ocusing knob to ocus on particular parts o the specimen. 4. Divide the length on the drawing by the length on the actual specimen. The result is the magnifcation. 9. Move the slide to bring the most interesting part o the size o image specimen into the centre o the eld o view. Magnication = ____ size o specimen 10. Turn the revolving nose piece to select the high power Example objective, then reocus using steps 57 again. The scale bar on the drawing o heart muscle tissue on 11. Adjust the illumination using the diaphragm. page 2 represents a length on the specimen o 20 m eye piece and is 10 mm long, which is 10,000 m. 10,000 Magnication = __ = 500 20 The magnication equation can be rearranged and used to nose piece calculate the actual size o a specimen i the magnication objective lens and size o the image are known. size o image stage coarse focusing Size o specimen = ___ magnication condenser lens knob Example and diaphragm ne focusing knob The length o the beta cell in the pancreatic islet on page 2 is 48mm, which is 48,000 m, and the magnication o the drawing is 4000. lamp 48,000 m Actual length o the cell = ___ = 12 m 4000 SCALE BARS A scale bar is a line added to a micrograph or a drawing to help to show the actual size o the structures. For example, a 10 m bar shows how large a 10 m object would appear. The gure below is a scanning electron micrograph (SEM) o a lea with the magnication and a scale bar both shown. 50 m S.I. size units 1000mm = 1 m 1000m = 1nm 1000nm = 1m Scanning electron micrograph o lea (x480) 4 C E LL B I O LO G Y Electron microscopes and ultrastructure RESOLUTION AND MAGNIFICATION TECHNOLOGY AND SCIENCE In every type o microscope magnifcation can be increased The diagram (below let) shows a simplifed version o until a point above which the image can no longer be ocused the technology o an electron microscope. The electron sharply. This is because the resolution o the microscope has microscope is a good example o an important trend in been exceeded. science improvements in technology or apparatus lead to Resolution is the ability o the microscope to show two close developments in scientifc research. objects separately in the image. The invention o the electron microscope led to a much The resolution o a microscope depends on the wavelength o greater understanding o the structure o cells and the the rays used to orm the image the shorter the wavelength discovery o many structures within living organisms. the higher the resolution. Electrons have a much shorter The detailed structure o the cell that was revealed by the wavelength than light, so electron microscopes have a electron microscope is known as ultrastructure. higher resolution than light microscopes. They can thereore produce a sharp image at much higher magnifcations. ULTRASTRUCTURE OF PALISADE CELLS Light Electron The electron micrograph below is an example o the detailed microscope microscope ultrastructure that the electron microscope reveals. Resolution 0.25 m 0.25 nm Chloroplast carries out photosynthesis. Magnifcation 500 500,000 Cell wall supports and protects the cell. Plasma membrance controls entry and exit o substances. Transmission electron microscopes (TEM) are used to view ultra-thin sections. (Names o parts o this microscope do Chloroplast Cell wall Plasma membrane not have to be memorized.) Scanning electron microscopes (SEM) produce an image o the suraces o structures. voltage feed electron gun vacuum electron beam anode condenser lens specimen objective lens intermediate lens projector lens Free ribosomes Nuclear membrane viewing port Free ribosomes synthesize cytoplasmic proteins. Nuclear membrane protects chromosomes. In the other parts o this cell there were many more uorescent chloroplasts and a large vacuole, indicating that the unction screen o this cell was photosynthesis. It is a palisade mesophyll cell rom the lea o a plant. C E LL B I O LO G Y 5 Prokaryotic cells STRUCTURE OF PROKARYOTIC CELLS SURFACE AREA TO VOLUME RATIOS Cells are divided into two types according to their structure, As the size o any object is increased, the ratio between the prokaryotic and eukaryotic. The frst cells to evolve were surace area and the volume decreases. Consider the surace prokaryotic and many organisms still have prokaryotic cells, area to volume ratio o cubes o varying size as an example. including all bacteria. The rate at which materials enter or leave a cell depends Prokaryotic cells have a relatively simple cell structure. on the surace area o the cell. However, the rate at which Eukaryotic cells are divided up by membranes into separate materials are used or produced depends on the volume. compartments such as the nucleus and mitochondria, A cell that becomes too large may not be able to take in essential whereas prokaryotic cells are not compartmentalized. materials or excrete waste substances quickly enough. Surace They do not have a nucleus, mitochondria or any other area to volume ratio is important in biology. It helps to explain membrane-bound organelles within their cytoplasm. many phenomena apart rom maximum cell sizes. DRAWING PROKARYOTIC CELLS cytoplasm cell wall nucleoid plasma (region membrane Two Salmonella bacteria alongside each other. Negative containing staining showing agella and short structures called pili which naked DNA) bacteria used to pull themselves close to each other pili 70S ribosomes Salmonella bacteria in a agellum thin section transmission electron micrograph BINARY FISSION IN PROKARYOTES Prokaryotic cells divide by a process called binary fission nucleoid (region this simply means splitting in ribosomes cell wall plasma membrane cytoplasm containing naked DNA) two. The bacterial chromosome is replicated so there are two identical copies. These are moved to opposite ends o the cell and the wall and plasma membrane are then pulled inwards so the cell pinches apart to orm two identical cells. Some prokaryotes can double in volume and divide by Escherichia coli ( 2m long) starting to divide binary ission every 30 minutes. 6 C E LL B I O LO G Y Eukaryotic cells STRUCTURE OF EUKARYOTIC CELLS DRAWING EUKARYOTIC CELLS Using a light microscope it is possible to see that The drawing shows the types o organelle that occur in eukaryotic eukaryotic cells have cytoplasm enclosed in a plasma cells. Chloroplasts and cell walls are part o plant cells but not membrane, like prokaryotic cells. However, unlike animal cells. prokaryotic cells, they usually contain a nucleus. Under the electron microscope details o much smaller structures within the cell are visible. This chromosomes is called the ultrastructure o a cell. There are a consisting of nuclear number o diferent types o organelle that orm DNA and histones membrane compartments in eukaryotic cells, each bounded by nuclear pore either one or two membranes: rough Organelles with a single membrane: endoplasmic Rough endoplasmic reticulum lysosome reticulum Smooth endoplasmic reticulum cell wall Golgi apparatus mitochondrion Lysosomes Vesicles and vacuoles chloroplast Organelles with a double membrane: cytoplasm Golgi apparatus Nucleus Mitochondrion vesicles plasma membrane Chloroplast Advantage of compartmentalization: PLANT CELL ANIMAL CELL Enzymes and substrates used in a process can be concentrated in a small area, with pH and other conditions at optimum levels and with no other enzymes that might disrupt the process. IDENTIFYING ORGANELLES AND DEDUCING FUNCTIONS The electron micrograph shows the structure o a cell in the pancreas. Golgi apparatus mitochondrion nucleus vesicle rough endoplasmic reticuluma The presence o large amounts o rough endoplasmic reticulum and many Golgi apparatuses shows that the main unction o this cell is to synthesize and secrete proteins, presumably the enzymes in pancreatic juice. C E LL B I O LO G Y 7 Models of membrane structure THE DAVSONDANIELLI MODEL THE SINGERNICOLSON MODEL In this model o membrane structure there is a bilayer o In the 1950s and 60s evidence accumulated that did not t phospholipids in the centre o the membrane with layers the DavsonDanielli model: o protein on either side. It was developed by Davson and 1. Freeze-racture electron micrographs showed that Danielli in the 1930s. globular proteins were present in the centre o the phospholipid bilayer (below). layer of protein phospholipid bilayer Reasons or the model: 1. Chemical analysis o membranes showed that they were composed o phospholipid and protein. 2. Evidence suggested that the plasma membrane o red 2. Analysis o membrane proteins showed that parts o blood cells has enough phospholipids in it to orm an their suraces were hydrophobic, so they would be area twice as large as the area o the plasma membrane, positioned in the bilayer and in some cases would suggesting a phospholipid bilayer. extend rom one side to the other. 3. Experiments showed that membranes orm a barrier to Non-polar amino acids in the the passage o some substances, despite being very centre of water-soluble proteins thin, and layers o protein could act as the barrier. Polar amino stabilize their structure. acids on the Testing the model: Non-polar amino acids surface of High magnication electron micrographs were rst produced proteins make cause proteins to remain in the 1950s. In these micrographs membranes appeared as them water embedded in membranes. two dark lines separated by a lighter band. soluble. This seemed to t the DavsonDanielli model, as proteins usually appear darker than phospholipids in electron Polar amino acids micrographs. The electron micrograph below shows create channels membranes both at the suraces o cells and around vesicles through which with the appearance that seemed to back up the Davson hydrophilic Danielli model. substances can Polar amino acids cause Electron micrograph of biological membranes diuse. Positively parts of membrane proteins charged R groups to protrude from the allow negatively membrane. Transmembrane charged ions through proteins have two such regions. and vice versa. 3. Fusion o cells with membrane proteins tagged with diferent coloured uorescent markers showed that these proteins can move within the membrane as the colours became mixed within a ew minutes o cell usion. red cell 40 fusion minutes green red and green mixed This evidence alsied the DavsonDanielli model. A new model was proposed in 1966 by Singer and Nicolson. This model is still used today. It is called either the SingerNicolson model or uid mosaic model. 8 C E LL B I O LO G Y Membrane structure FLUID MOSAIC MODEL OF MEMBRANE STRUCTURE Phospholipid molecules are shown as an oval with two parallel lines because they have a phosphate head with two atty acid tails attached. Proteins occupy a range o dierent positions in the membrane. Integral proteins are embedded in the phospholipid bilayer. Peripheral proteins are attached to an outer surace o the membrane. Glycoproteins have sugar units attached on the outer surace o the membrane. glycoprotein hydrophilic hydrophobic cholesterol phosphate head hydrocarbon tail pump or channel protein phospholipid bilayer integral proteins embedded peripheral protein in the phospholipid bilayer on the surface of the membrane PHOSPHOLIPIDS CHOLESTEROL Phospholipids are the basic component o all biological Cholesterol is a component o animal cell membranes. membranes. Phospholipid molecules are amphipathic. Most o the cholesterol molecule is hydrophobic but, like This means that part o the molecule is attracted to water phospholipids, there is one hydrophilic end; so cholesterol (hydrophilic) and part is not attracted to water (hydrophobic). ts between phospholipids in the membrane. The phosphate head is hydrophilic and the two atty acid Cholesterol restricts the movement o phospholipid tails, which are composed o hydrocarbon chains, are molecules. It thereore reduces the fuidity o the hydrophobic. When phospholipids are mixed with water they membrane. It also reduces the permeability o the naturally become arranged into bilayers, with the hydrophilic membrane to hydrophilic particles such as sodium ions heads acing outwards and making contact with the water and and hydrogen ions. This is important, as animal cells need the hydrocarbon tails acing inwards away rom the water. The to maintain concentration diferences o these ions across attraction between the hydrophobic tails in the centre o the their membranes, so difusion through the membrane must phospholipid bilayer and between the hydrophilic heads and be restricted. the surrounding water makes membranes very stable. MEMBRANE PROTEINS Membrane proteins are diverse in structure, unction and position in the membrane. The diagram above shows a glycoprotein, used or cell-to-cell communication. The diagram below shows examples o other membrane proteins. Insulin receptor an Cytochrome c a Calcium pump an integral integral protein that peripheral protein used protein for active transport is a hormone receptor for electron transport of calcium ions e- OUTSIDE INSIDE Nicotinic acetylcholine receptor an Cadherin an integral Cytochrome oxidase an integral protein that is both a receptor protein used for integral protein that is an for a neuro transmitter and a channel cell-to-cell adhesion immobilized enzyme for facilitated diusion of sodium ions C E LL B I O LO G Y 9 Difusion and acilitated difusion DIFFUSION SIMPLE AND FACILITATED DIFFUSION Solids, liquids and gases consist o particles atoms, Membranes allow some substances to difuse through but ions and molecules. In liquids and gases, these particles not others they are partially permeable. Some o these are in continual motion. The direction o movement is substances move between the phospholipid molecules in random. I particles are evenly spread then their movement the membrane this is simple difusion. Other substances in all directions is even and there is no net movement are unable to pass between the phospholipids. To allow they remain evenly spread despite continually moving. these substances to difuse through membranes, channel Sometimes particles are unevenly spread there is a proteins are needed. This is called acilitated difusion. higher concentration in one region than another. This Channel proteins are specic they only allow one type o causes difusion. substance to pass through. For example, chloride channels Difusion is the passive movement o particles rom a region only allow chloride ions to pass through. Cells can control o higher concentration to a region o lower concentration, as whether substances pass through their plasma membranes, a result o the random motion o particles. by the types o channel protein that are inserted into the membrane. Cells cannot control the direction o movement. Difusion occurs because more particles move rom Facilitated difusion always occurs rom a region o higher the region o higher concentration to the region o lower concentration to a region o lower concentration. Both simple concentration than move in the opposite direction. Difusion and acilitated difusion are passive processes no energy can occur across membranes i there is a concentration has to be used by the cell to make them occur. gradient and the membrane is permeable to the particle. For example, membranes are reely permeable to oxygen, There are sodium and potassium channel proteins in the so i there is a lower concentration o oxygen inside a cell membranes o neurons that open and close, depending on than outside, it will difuse into the cell. Membranes are not the voltage across the membrane. They are voltage-gated permeable to cellulose, so it does not difuse across. channels and are used to transmit nerve impulses. membrane consisting higher lower membrane containing of phospholipid bilayer concentration concentration channel proteins solute able to diuse facilitated diusion through membrane solute unable to diuse through membrane through membrane containing channel proteins STRUCTURE AND FUNCTION OF 2 Channel briey open net negative charge POTASSIUM CHANNELS IN AXONS - - - - + - - - - OUTSIDE The axons o neurons contain potassium channels that are + + + + + + used during an action potential. They are closed when the axon + is polarized but open in response to depolarization o the axon membrane, allowing K+ ions to exit by acilitated difusion, which + + + + + + + INSIDE OF AXON repolarizes the axon. Potassium channels only remain open or a very short time beore a globular sub-unit blocks the pore. The K+ ions net positive charge channel then returns to its original closed conormation. 1 Channel closed 3 Channel closed by ball and chain + + + + + + + + - - - - - - - - + + + + + + + + ++ + + + + ++ - - - - - - - - - + + + + + + + + chain net negative charge inside hydrophobic core ball hydrophilic outer the axon and net positive of the membrane parts of the membrane charge outside 10 C E LL B I O LO G Y Osmosis WATER MOVEMENT BY OSMOSIS Plasma membranes are usually reely permeable to water. the membrane is impermeable to them The passive movement o water across membranes is region of lower solute diferent rom difusion across membranes, because water is concentration ( in this the solvent. A solvent is a liquid in which particles dissolve. case pure water) Dissolved particles are called solutes. The direction in which water moves is due to the concentration o solutes, rather than the concentration o water molecules, so it is called partially permeable osmosis, rather than difusion. membrane Osmosis is the passive movement o water molecules rom region of higher a region o lower solute concentration to a region o higher solute concentration solute concentration, across a partially permeable membrane. Attractions between solute particles and water molecules are Water molecules move in and out through the membrane the reason or water moving to regions with a higher solute but more move in than out. There is a net movement from concentration. the region of lower solute concentration to the region of higher solute concentration ESTIMATING OSMOLARITY SAMPLE OSMOLARITY RESULTS The osmolarity o a solution is the number o moles o solute particles per unit volume o solution. Pure water has an 20 osmolarity o zero. The greater the concentration o solutes, Sodium chloride concentration % Mass change the higher the osmolarity. 10 I two solutions at equal pressure but with diferent osmolarity (mol/litre) 0 are separated by a partially permeable membrane, water will 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 move by osmosis rom the solution with the lower osmolarity 10 PUMPKIN to the solution with the higher osmolarity. Plant cells absorb water rom a surrounding solution i their osmolarity is higher 20 SWEET than that o the solution (i.e. the surrounding solution is POTATO hypotonic) or lose water i their osmolarity is lower (i.e. the solution is hypertonic). This principle can be used to estimate The estimated osmolarity o the pumpkin is equal to the osmolarity o a type o plant tissue, such as potato. 0.55 moles / litre NaCl solution, which is 1.1 osmoles / litre. Method: 1. Prepare a series o solutions with a suitable range o solute concentrations, such as 0.0, 0.1, 0.2, 0.3, 0.4 and ACCURACY IN OSMOSIS EXPERIMENTS 0.5 moles/litre. Estimates o osmolarity rom this experiment will only be as accurate as the quantitative measurements, so it is essential 2. Cut the tissue into samples o equal size and shape. or these to be as accurate as possible: 3. Find the mass o each sample, using an electronic balance. the volume o water used or making solutions should be 4. Bathe tissue samples in each o the range o solutions measured with a volumetric ask or long enough to get measurable mass changes, the initial and nal mass o tissue samples should be usually between 10 and 60 minutes. measured with the same electronic balance that is 5. Remove the tissue samples rom the bathing solutions, accurate to 0.01 grams (10 mg). dry them and nd their mass again. 6. Calculate percentage mass change using this ormula: (nal mass initial mass) AVOIDING OSMOSIS IN DONOR ORGANS % change = ______ 100 Osmosis can cause cells in human tissues or organs to swell initial mass 7. Plot the results on a graph. up and burst, or to shrink due to gain or loss o water by osmosis. To prevent this, tissues or organs used in medical 8. Read of the solute concentration which would give no procedures such as kidney transplants must be bathed in a mass change. It has the same osmolarity as the tissue. solution with the same osmolarity as human cytoplasm. NB The osmolarity o a glucose solution is equal to its molarity because glucose remains as single molecules A solution o salts called isotonic saline is used or some when it dissolves. procedures. The osmolarity o a sodium chloride solution is double its Donor organs are surrounded by isotonic slush when they molarity because one mole o NaCl gives two moles o ions are being transported, with the low temperatures helping when it dissolves one mole o Na + and one mole o Cl -. to keep them in a healthy state. C E LL B I O LO G Y 11 Active transport PUMP PROTEINS AND ACTIVE TRANSPORT Active transport is the movement o substances across membranes using energy rom ATP. Active transport can move substances against the concentration gradient rom a region o lower to a region o higher concentration. Protein pumps in the membrane are used or active transport. Each pump only transports particular substances, so cells can control 1. Particle enters 2. Particle binds to 3. Energy from ATP 4. Particle is released what is absorbed and what is the pump from is used to change on the side with a expelled. Pumps work in a specic the side with Other types of the shape of the higher concentration direction the substance can only a lower particle cannot pump and the pump then enter the pump on one side and concentration bind returns to its original can only exit on the other side. shape STRUCTURE AND FUNCTION OF SODIUMPOTASSIUM PUMPS IN AXONS The axons o neurons contain a pump In the centre o the pump there are two protein that moves sodium ions and binding sites or K+ ions and three or potassium ions across the membrane. Na + ions. The pump has two alternate As sodium and potassium are pumped in states. In one, there is access to the 2K+ opposite directions it is an antiporter. The 3Na + binding sites rom the outer side o energy that is required or the pumping OUTSIDE the membrane and there is a stronger is obtained by converting ATP to ADP and attraction to K+ ions, so Na + are phosphate, so it is an ATPase. It is known discharged rom the cell and K+ bind. to biochemists as Na + /K+ -ATPase. One In the other state there is access to the ATP provides enough energy to pump binding sites rom inside and there is a two potassium ions in and three sodium INSIDE stronger attraction or Na + ions, so ions out o the cell. The concentration K+ ions are discharged into the cell and gradients generated by this active 3Na + Na + bind. Energy rom ATP causes the transport are needed or the transmission 2K+ switch rom one state to the other and o nerve impulses in axons. then back again. TRANSPORT USING VESICLES The uidity o 1. Proteins are 3. The Golgi membranes synthesized by from the rER and apparatus the Golgi apparatus allows them ribosomes and then carry the proteins to move and enter the rough to the Golgi proteins proteins to the plasma change shape. endoplasmic apparatus membrane Small pieces ENDOCYTOSIS reticulum o membrane EXOCYTOSIS 1. Part of the plasma can be pinched 1. Vesicles fuse with the membrane is pulled of the plasma plasma membrane inwards membrane to create a vesicle 2. A 2. The contents of the containing becomes enclosed vesicle are expelled some material when a vesicle is rom outside 3. The membrane then the cell. This is endocytosis. 3. Vesicles can then move Vesicles can through the cytoplasm also move to carrying their contents the plasma membrane and use with it, releasing the contents o the vesicle outside the cell This is exocytosis. Vesicles are used to move materials rom one part o the cell to another. For example, vesicles move proteins rom the rough ER to the Golgi apparatus. 12 C E LL B I O LO G Y Origins of cells CELL DIVISION AND CELL ORIGINS PASTEURS EXPERIMENTS Until the 19th century some biologists believed that The general principle that cells can only come rom pre- lie could appear in non-living material. This was called existing ones was tested repeatedly by scientists in the 18th spontaneous generation. There is no evidence that living and 19th centuries. It was the experiments o Louis Pasteur cells can be ormed on Earth today except by division o that veried the principle beyond reasonable doubt. pre-existing cells. Spontaneous generation o cells is not The most amous o Pasteurs experiments involved the use currently possible. o swan-necked asks. He placed samples o broth in asks with long necks and then melted the glass o the necks and bent it into a variety o shapes. Pasteur then boiled the broth ORIGINS OF THE FIRST CELLS in some o the asks to kill any organisms present but let The general principle that cells are only ormed by division o others unboiled as controls. Fungi and other organisms soon pre-existing cells can be used to trace lie back to its origins. appeared in the unboiled asks but not in the boiled ones, All o the billions o cells in a human or other multicellular even ater long periods o time. The broth in the asks was organism are ormed by repeated cell division, starting with in contact with air, which it had been suggested was needed a single cell ormed by reproduction. We can trace the origins or spontaneous generation, yet no spontaneous generation o cells back through the generations and through hundreds occurred. Pasteur snapped the necks o some o the asks to o millions o years o evolution. Eventually we must reach leave a shorter vertical neck. Organisms were soon apparent the rst cells, as lie has not always existed on Earth. Beore in these asks and decomposed the broth. these cells existed there was only non-living material on Earth. One o the great challenges in biology is to understand how the rst living cells evolved rom non-living matter and why spontaneous generation could take place then but not now. It is a remarkable act that the sixty-our codons o the genetic code have the same meanings in the cells o all organisms, apart rom minor variations. The universality o the genetic code suggests strongly that all lie evolved rom the same He concluded that the swan necks prevented organisms original cells. Minor dierences in the genetic code will have rom the air getting into the asks and that no organisms accrued since the common origin o lie on Earth. appeared spontaneously. THE ENDOSYMBIOTIC THEORY Symbiosis is two organisms living together. With HOST CELL endosymbiosis a larger cell takes in a smaller cell by endocytosis, so the smaller cell is inside a vesicle in the nucleus AEROBIC BACTERIUM cytoplasm o the larger cell. Instead o the smaller cell being digested, it is kept alive and perorms a useul unction or the larger cell. The smaller cell divides at least as requently PHOTOSYNTHETIC as the larger cell so all cells produced by division o the BACTERIUM larger cell contain one or more o the smaller cells inside its HETEROTROPHIC EUKARYOTES vesicle. According to the endosymbiotic theory, this process e.g. ANIMALS happened at least twice during the origin o eukaryotic cells. 1. A cell that respired anaerobically took in a bacterium mitochondrion that respired aerobically, supplying both itsel and the larger cell with energy in the orm o ATP. This gave the larger cell a competitive advantage because aerobic AUTOTROPHIC PHOTOSYNTHETIC respiration is more efcient than anaerobic. Gradually EUKARYOTES e.g. PLANTS the aerobic bacterium evolved into mitochondria and the larger cell evolved into heterotrophic eukaryotes chloroplast alive today such as animals. 2. A heterotrophic cell took in a smaller photosynthetic bacterium, which supplied it with organic compounds, thus making it an autotroph. The photosynthetic prokaryote evolved into chloroplasts and the larger cell evolved into photosynthetic eukaryotes alive today such as plants. This theory explains the characteristics o mitochondria and chloroplasts: They grow and divide like cells. They have a naked loop o DNA, like prokaryotes. They synthesize some o their own proteins using 70S ribosomes, like prokaryotes. They have double membranes, as expected when cells are taken into a vesicle by endocytosis. C E LL B I O LO G Y 13 Mitosis CHROMOSOMES AND CONDENSATION CHROMATIDS AND CENTROMERES In eukaryotes nearly all the DNA o a cell is stored in the The chromosomes become condensed enough during the nucleus. A human nucleus contains 2 metres o DNA and yet early stages o mitosis to be visible with a light microscope. the nucleus is only about 5 m in diameter. It ts in quite At this stage o mitosis each chromosome is a double easily because the DNA molecule is so narrow its width is structure. The two parts o the chromosome are called 2 nm, which is 0.002 m. A DNA molecule is ar too small to sister chromatids. They are held together at one point by a be visible with a light microscope. structure known as a centromere. In eukaryotes the DNA molecules have proteins attached The term sister indicates that the two chromatids contain an to them, orming structures called chromosomes. During identical DNA molecule, produced by DNA replication beore mitosis the chromosomes become shorter and atter. This the start o mitosis. During mitosis the centromere divides is called condensation and occurs by a complex process o and the sister chromatids separate. From then onwards they coiling, known as supercoiling. are reerred to as chromosomes rather than chromatids. THE PHASES OF MITOSIS 1 Early prophase 2 Late prophase 3 Metaphase Each chromosome Spindle Spindle consists of two microtubules microtubules identical extend from Spindle are growing chromatids each pole to microtubules formed by DNA the equator from both replication in The nuclear poles are Chromosomes interphase and membrane has attached are becoming held together broken down and to each shorter and by a centromere chromosomes centromere, fatter by have moved to on opposite supercoiling the equator sides 4 Anaphase All chromosomes 5 Early telophase 6 Late telophase have reached the poles and The centromeres nuclear membranes Spindle have divided form around them microtubules and the break down The cell chromatids Spindle divides Chromosomes have become microtubules (cytokinesis) uncoil and chromosomes pull the to form two are no longer genetically cells with individually identical genetically visible chromosomes identical to opposite poles nuclei MITOTIC INDEX CYTOKINESIS The mitotic index is the ratio between the Cytokinesis is the division o number o cells in mitosis in a tissue and the the cytoplasm to orm two cells. total number o observed cells. It occurs ater mitosis and is number _o cells in_ mitosis diferent in plant and animal cells. Mitotic index = _ _ _ _ total number o cells In plant cells a new cell wall Count the total number o cells in the is ormed across the equator micrograph and then count the number o cells o the cell, with plasma in any o the our phases o mitosis. The mitotic membrane on both sides. index can then be calculated. This divides the cell in two. The mitotic index is used by doctors to predict In animal cells the plasma how rapidly a tumour will grow and thereore membrane at the equator is what treatment is needed. A high index indicates pulled inwards until it meets a ast-growing tumour. One cell in each o the telophase metaphase in the centre o the cell, our stages o mitosis is identied right. anaphase prophase dividing it in two. 14 C E LL B I O LO G Y Cell cycles and cancer THE CELL CYCLE IN EUKARYOTES I n t e rp h a s e The cell cycle is the sequence o events between one cell division and the next. It has two main phases: interphase S phase and cell division. Interphase is a very active phase in the lie o a cell when many metabolic reactions occur. Some o G2 G1 these, such as the reactions o cell respiration, also occur during cell division, but DNA replication in the nucleus and protein synthesis in the cytoplasm only happen during THE Cytokinesis interphase. CELL During interphase the numbers o mitochondria in the CYCLE Pro p se cytoplasm increase, as they grow and divide. In plant cells
